32 results on '"van der Sluijs, Pleuntje J."'
Search Results
2. Landscape of mSWI/SNF chromatin remodeling complex perturbations in neurodevelopmental disorders
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Valencia, Alfredo M., Sankar, Akshay, van der Sluijs, Pleuntje J., Satterstrom, F. Kyle, Fu, Jack, Talkowski, Michael E., Vergano, Samantha A. Schrier, Santen, Gijs W. E., and Kadoch, Cigall
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- 2023
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3. Elucidating the clinical and molecular spectrum of SMARCC2-associated NDD in a cohort of 65 affected individuals
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Bosch, Elisabeth, Popp, Bernt, Güse, Esther, Skinner, Cindy, van der Sluijs, Pleuntje J., Maystadt, Isabelle, Pinto, Anna Maria, Renieri, Alessandra, Bruno, Lucia Pia, Granata, Stefania, Marcelis, Carlo, Baysal, Özlem, Hartwich, Dewi, Holthöfer, Laura, Isidor, Bertrand, Cogne, Benjamin, Wieczorek, Dagmar, Capra, Valeria, Scala, Marcello, De Marco, Patrizia, Ognibene, Marzia, Jamra, Rami Abou, Platzer, Konrad, Carter, Lauren B., Kuismin, Outi, van Haeringen, Arie, Maroofian, Reza, Valenzuela, Irene, Cuscó, Ivon, Martinez-Agosto, Julian A., Rabani, Ahna M., Mefford, Heather C., Pereira, Elaine M., Close, Charlotte, Anyane-Yeboa, Kwame, Wagner, Mallory, Hannibal, Mark C., Zacher, Pia, Thiffault, Isabelle, Beunders, Gea, Umair, Muhammad, Bhola, Priya T., McGinnis, Erin, Millichap, John, van de Kamp, Jiddeke M., Prijoles, Eloise J., Dobson, Amy, Shillington, Amelle, Graham, Brett H., Garcia, Evan-Jacob, Galindo, Maureen Kelly, Ropers, Fabienne G., Nibbeling, Esther A.R., Hubbard, Gail, Karimov, Catherine, Goj, Guido, Bend, Renee, Rath, Julie, Morrow, Michelle M., Millan, Francisca, Salpietro, Vincenzo, Torella, Annalaura, Nigro, Vincenzo, Kurki, Mitja, Stevenson, Roger E., Santen, Gijs W.E., Zweier, Markus, Campeau, Philippe M., Severino, Mariasavina, Reis, André, Accogli, Andrea, and Vasileiou, Georgia
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- 2023
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4. Prevalence of comorbidities in individuals with neurodevelopmental disorders from the aggregated phenomics data of 51,227 pediatric individuals
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Dingemans, Alexander J. M., primary, Jansen, Sandra, additional, van Reeuwijk, Jeroen, additional, de Leeuw, Nicole, additional, Pfundt, Rolph, additional, Schuurs-Hoeijmakers, Janneke, additional, van Bon, Bregje W., additional, Marcelis, Carlo, additional, Ockeloen, Charlotte W., additional, Willemsen, Marjolein, additional, van der Sluijs, Pleuntje J., additional, Santen, Gijs W. E., additional, Kooy, R. Frank, additional, Vulto-van Silfhout, Anneke T., additional, Kleefstra, Tjitske, additional, Koolen, David A., additional, Vissers, Lisenka E. L. M., additional, and de Vries, Bert B. A., additional
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- 2024
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5. Correction: Putting genome-wide sequencing in neonates into perspective
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van der Sluijs, Pleuntje J., Aten, Emmelien, Barge-Schaapveld, Daniela Q. C. M., Bijlsma, Emilia K., Bökenkamp-Gramann, Regina, Kaat, Laura Donker, van Doorn, Remco, van de Putte, Dietje Fransen, van Haeringen, Arie, ten Harkel, Arend D. J., Hilhorst-Hofstee, Yvonne, Hoffer, Mariette J. V., den Hollander, Nicolette S., van Ierland, Yvette, Koopmans, Marije, Kriek, Marjolein, Moghadasi, Setareh, Nibbeling, Esther A. R., Peeters-Scholte, Cacha M. P. C. D., Potjer, Thomas P., van Rij, Maartje, Ruivenkamp, Claudia A. L., Rutten, Julie W., Steggerda, Sylke J., Suerink, Manon, Tan, Ratna N. G. B., van der Tuin, Karin, Visser, Remco, van der Werf –’t Lam, Anne-Sophie, Williams, Monique, Witlox, Ruben, and Santen, Gijs W. E.
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- 2019
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6. The ARID1B spectrum in 143 patients: from nonsyndromic intellectual disability to Coffin–Siris syndrome
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van der Sluijs, Pleuntje J., Jansen, Sandra, Vergano, Samantha A., Adachi-Fukuda, Miho, Alanay, Yasemin, AlKindy, Adila, Baban, Anwar, Bayat, Allan, Beck-Wödl, Stefanie, Berry, Katherine, Bijlsma, Emilia K., Bok, Levinus A., Brouwer, Alwin F. J., van der Burgt, Ineke, Campeau, Philippe M., Canham, Natalie, Chrzanowska, Krystyna, Chu, Yoyo W. Y., Chung, Brain H. Y., Dahan, Karin, De Rademaeker, Marjan, Destree, Anne, Dudding-Byth, Tracy, Earl, Rachel, Elcioglu, Nursel, Elias, Ellen R., Fagerberg, Christina, Gardham, Alice, Gener, Blanca, Gerkes, Erica H., Grasshoff, Ute, van Haeringen, Arie, Heitink, Karin R., Herkert, Johanna C., den Hollander, Nicolette S., Horn, Denise, Hunt, David, Kant, Sarina G., Kato, Mitsuhiro, Kayserili, Hülya, Kersseboom, Rogier, Kilic, Esra, Krajewska-Walasek, Malgorzata, Lammers, Kylin, Laulund, Lone W., Lederer, Damien, Lees, Melissa, López-González, Vanesa, Maas, Saskia, Mancini, Grazia M. S., Marcelis, Carlo, Martinez, Francisco, Maystadt, Isabelle, McGuire, Marianne, McKee, Shane, Mehta, Sarju, Metcalfe, Kay, Milunsky, Jeff, Mizuno, Seiji, Moeschler, John B., Netzer, Christian, Ockeloen, Charlotte W., Oehl-Jaschkowitz, Barbara, Okamoto, Nobuhiko, Olminkhof, Sharon N. M., Orellana, Carmen, Pasquier, Laurent, Pottinger, Caroline, Riehmer, Vera, Robertson, Stephen P., Roifman, Maian, Rooryck, Caroline, Ropers, Fabienne G., Rosello, Monica, Ruivenkamp, Claudia A. L., Sagiroglu, Mahmut S., Sallevelt, Suzanne C. E. H., Sanchis Calvo, Amparo, Simsek-Kiper, Pelin O., Soares, Gabriela, Solaeche, Lucia, Sonmez, Fatma Mujgan, Splitt, Miranda, Steenbeek, Duco, Stegmann, Alexander P. A., Stumpel, Constance T. R. M., Tanabe, Saori, Uctepe, Eyyup, Utine, G. Eda, Veenstra-Knol, Hermine E., Venkateswaran, Sunita, Vilain, Catheline, Vincent-Delorme, Catherine, Vulto-van Silfhout, Anneke T., Wheeler, Patricia, Wilson, Golder N., Wilson, Louise C., Wollnik, Bernd, Kosho, Tomoki, Wieczorek, Dagmar, Eichler, Evan, Pfundt, Rolph, de Vries, Bert B. A., Clayton-Smith, Jill, and Santen, Gijs W. E.
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- 2019
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7. Putting genome-wide sequencing in neonates into perspective
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van der Sluijs, Pleuntje J., Aten, Emmelien, Barge-Schaapveld, Daniela Q. C. M., Bijlsma, Emilia K., Bökenkamp-Gramann, Regina, Donker Kaat, Laura, van Doorn, Remco, van de Putte, Dietje Fransen, van Haeringen, Arie, ten Harkel, Arend D. J., Hilhorst-Hofstee, Yvonne, Hoffer, Mariette J. V., den Hollander, Nicolette S., van Ierland, Yvette, Koopmans, Marije, Kriek, Marjolein, Moghadasi, Setareh, Nibbeling, Esther A. R., Peeters-Scholte, Cacha M. P. C. D., Potjer, Thomas P., van Rij, Maartje, Ruivenkamp, Claudia A. L., Rutten, Julie W., Steggerda, Sylke J., Suerink, Manon, Tan, Ratna N. G. B., van der Tuin, Karin, Visser, Remco, van der Werf –’t Lam, Anne-Sophie, Williams, Monique, Witlox, Ruben, and Santen, Gijs W. E.
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- 2019
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8. Elucidating the clinical and molecular spectrum ofSMARCC2-associated NDD in a cohort of 65 affected individuals
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Bosch, Elisabeth, primary, Popp, Bernt, additional, Güse, Esther, additional, Skinner, Cindy, additional, van der Sluijs, Pleuntje J., additional, Maystadt, Isabelle, additional, Pinto, Anna Maria, additional, Renieri, Alessandra, additional, Bruno, Lucia Pia, additional, Granata, Stefania, additional, Marcelis, Carlo, additional, Baysal, Özlem, additional, Hartwich, Dewi, additional, Holthöfer, Laura, additional, Isidor, Bertrand, additional, Cogne, Benjamin, additional, Wieczorek, Dagmar, additional, Capra, Valeria, additional, Scala, Marcello, additional, De Marco, Patrizia, additional, Ognibene, Marzia, additional, Jamra, Rami Abou, additional, Platzer, Konrad, additional, Carter, Lauren B., additional, Kuismin, Outi, additional, van Haeringen, Arie, additional, Maroofian, Reza, additional, Valenzuela, Irene, additional, Cuscò, Ivon, additional, Martinez-Agosto, Julian A., additional, Rabani, Ahna M., additional, Mefford, Heather C., additional, Pereira, Elaine M., additional, Close, Charlotte, additional, Anyane-Yeboa, Kwame, additional, Wagner, Mallory, additional, Hannibal, Mark C., additional, Zacher, Pia, additional, Thiffault, Isabelle, additional, Beunders, Gea, additional, Umair, Muhammad, additional, Bhola, Priya T., additional, McGinnis, Erin, additional, Millichap, John, additional, van de Kamp, Jiddeke M, additional, Prijoles, Eloise J., additional, Dobson, Amy, additional, Shillington, Amelle, additional, Graham, Brett H., additional, Garcia, Evan-Jacob, additional, Galindo, Maureen Kelly, additional, Ropers, Fabienne G., additional, Nibbeling, Esther AR, additional, Hubbard, Gail, additional, Karimov, Catherine, additional, Goj, Guido, additional, Bend, Renee, additional, Rath, Julie, additional, Morrow, Michelle M, additional, Millan, Francisca, additional, Salpietro, Vincenzo, additional, Torella, Annalaura, additional, Nigro, Vincenzo, additional, Kurki, Mitja, additional, Stevenson, Roger E, additional, Santen, Gijs W.E., additional, Zweier, Markus, additional, Campeau, Philippe M., additional, Severino, Mariasavina, additional, Reis, André, additional, Accogli, Andrea, additional, and Vasileiou, Georgia, additional
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- 2023
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9. Discovering a new part of the phenotypic spectrum of Coffin-Siris syndrome in a fetal cohort
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van der Sluijs, Pleuntje J., primary, Joosten, Marieke, additional, Alby, Caroline, additional, Attié-Bitach, Tania, additional, Gilmore, Kelly, additional, Dubourg, Christele, additional, Fradin, Mélanie, additional, Wang, Tianyun, additional, Kurtz-Nelson, Evangeline C., additional, Ahlers, Kaitlyn P., additional, Arts, Peer, additional, Barnett, Christopher P., additional, Ashfaq, Myla, additional, Baban, Anwar, additional, van den Born, Myrthe, additional, Borrie, Sarah, additional, Busa, Tiffany, additional, Byrne, Alicia, additional, Carriero, Miriam, additional, Cesario, Claudia, additional, Chong, Karen, additional, Cueto-González, Anna Maria, additional, Dempsey, Jennifer C., additional, Diderich, Karin E.M., additional, Doherty, Dan, additional, Farholt, Stense, additional, Gerkes, Erica H., additional, Gorokhova, Svetlana, additional, Govaerts, Lutgarde C.P., additional, Gregersen, Pernille A., additional, Hickey, Scott E., additional, Lefebvre, Mathilde, additional, Mari, Francesca, additional, Martinovic, Jelena, additional, Northrup, Hope, additional, O’Leary, Melanie, additional, Parbhoo, Kareesma, additional, Patrier, Sophie, additional, Popp, Bernt, additional, Santos-Simarro, Fernando, additional, Stoltenburg, Corinna, additional, Thauvin-Robinet, Christel, additional, Thompson, Elisabeth, additional, Vulto-van Silfhout, Anneke T., additional, Zahir, Farah R., additional, Scott, Hamish S., additional, Earl, Rachel K., additional, Eichler, Evan E., additional, Vora, Neeta L., additional, Wilnai, Yael, additional, Giordano, Jessica L., additional, Wapner, Ronald J., additional, Rosenfeld, Jill A., additional, Haak, Monique C., additional, and Santen, Gijs W.E., additional
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- 2023
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10. Elucidating the clinical and molecular spectrum of SMARCC2-associated NDD in a cohort of 65 affected individuals
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Bosch, Elisabeth; https://orcid.org/0000-0002-4952-2016, Popp, Bernt; https://orcid.org/0000-0002-3679-1081, Güse, Esther, Skinner, Cindy, van der Sluijs, Pleuntje J; https://orcid.org/0000-0002-1174-2806, Maystadt, Isabelle, Pinto, Anna Maria, Renieri, Alessandra, Bruno, Lucia Pia, Granata, Stefania, Marcelis, Carlo, Baysal, Özlem, Hartwich, Dewi, Holthöfer, Laura, Isidor, Bertrand, Cogné, Benjamin; https://orcid.org/0000-0002-5503-6292, Wieczorek, Dagmar, Capra, Valeria, Scala, Marcello, De Marco, Patrizia, Ognibene, Marzia, Abou Jamra, Rami; https://orcid.org/0000-0002-1542-1399, Platzer, Konrad, Carter, Lauren B, Kuismin, Outi, van Haeringen, Arie, Maroofian, Reza; https://orcid.org/0000-0001-6763-1542, Valenzuela, Irene, Cuscó, Ivon, Martinez-Agosto, Julian A, et al, Zweier, Markus; https://orcid.org/0000-0001-8290-0413, Bosch, Elisabeth; https://orcid.org/0000-0002-4952-2016, Popp, Bernt; https://orcid.org/0000-0002-3679-1081, Güse, Esther, Skinner, Cindy, van der Sluijs, Pleuntje J; https://orcid.org/0000-0002-1174-2806, Maystadt, Isabelle, Pinto, Anna Maria, Renieri, Alessandra, Bruno, Lucia Pia, Granata, Stefania, Marcelis, Carlo, Baysal, Özlem, Hartwich, Dewi, Holthöfer, Laura, Isidor, Bertrand, Cogné, Benjamin; https://orcid.org/0000-0002-5503-6292, Wieczorek, Dagmar, Capra, Valeria, Scala, Marcello, De Marco, Patrizia, Ognibene, Marzia, Abou Jamra, Rami; https://orcid.org/0000-0002-1542-1399, Platzer, Konrad, Carter, Lauren B, Kuismin, Outi, van Haeringen, Arie, Maroofian, Reza; https://orcid.org/0000-0001-6763-1542, Valenzuela, Irene, Cuscó, Ivon, Martinez-Agosto, Julian A, et al, and Zweier, Markus; https://orcid.org/0000-0001-8290-0413
- Abstract
Purpose: Coffin-Siris and Nicolaides-Baraitser syndromes, are recognisable neurodevelopmental disorders caused by germline variants in BAF complex subunits. The SMARCC2 BAFopathy was recently reported. Herein, we present clinical and molecular data on a large cohort. Methods: Clinical symptoms for 41 novel and 24 previously published affected individuals were analyzed using the Human Phenotype Ontology. For genotype-phenotype correlation, molecular data were standardized and grouped into non-truncating and likely gene-disrupting (LGD) variants. Missense variant protein expression and BAF subunit interactions were examined using 3D protein modeling, co-immunoprecipitation, and proximity-ligation assays. Results: Neurodevelopmental delay with intellectual disability, muscular hypotonia and behavioral disorders were the major manifestations. Clinical hallmarks of BAFopathies were rare. Clinical presentation differed significantly, with LGD variants being predominantly inherited and associated with mildly reduced or normal cognitive development, while non-truncating variants were mostly de novo and presented with severe developmental delay. These distinct manifestations and non-truncating variant clustering in functional domains suggest different pathomechanisms. In vitro testing showed decreased protein expression for N-terminal missense variants similar to LGD. Conclusion: This study improved SMARCC2 variant classification and identified discernible SMARCC2-associated phenotypes for LGD and non-truncating variants, which were distinct from other BAFopathies. The pathomechanism of most non-truncating variants has yet to be investigated.
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- 2023
11. PhenoScore: AI-based phenomics to quantify rare disease and genetic variation
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Dingemans, Alexander J M, primary, Hinne, Max, additional, Truijen, Kim M G, additional, Goltstein, Lia, additional, van Reeuwijk, Jeroen, additional, de Leeuw, Nicole, additional, Schuurs-Hoeijmakers, Janneke, additional, Pfundt, Rolph, additional, Diets, Illja J, additional, den Hoed, Joery, additional, de Boer, Elke, additional, Coenen-van der Spek, Jet, additional, Jansen, Sandra, additional, van Bon, Bregje W, additional, Jonis, Noraly, additional, Ockeloen, Charlotte, additional, Vulto-van Silfhout, Anneke T, additional, Kleefstra, Tjitske, additional, Koolen, David A, additional, Van Esch, Hilde, additional, Lyon, Gholson J, additional, Alkuraya, Fowzan S, additional, Rauch, Anita, additional, Marom, Ronit, additional, Baralle, Diana, additional, van der Sluijs, Pleuntje J, additional, Santen, Gijs W E, additional, Kooy, R Frank, additional, van Gerven, Marcel A J, additional, Vissers, Lisenka E L M, additional, and de Vries, Bert B A, additional
- Published
- 2022
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12. Functional correlation of genome‐wide DNA methylation profiles in genetic neurodevelopmental disorders
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Levy, Michael A., primary, Relator, Raissa, additional, McConkey, Haley, additional, Pranckeviciene, Erinija, additional, Kerkhof, Jennifer, additional, Barat‐Houari, Mouna, additional, Bargiacchi, Sara, additional, Biamino, Elisa, additional, Palomares Bralo, María, additional, Cappuccio, Gerarda, additional, Ciolfi, Andrea, additional, Clarke, Angus, additional, DuPont, Barbara R., additional, Elting, Mariet W., additional, Faivre, Laurence, additional, Fee, Timothy, additional, Ferilli, Marco, additional, Fletcher, Robin S., additional, Cherick, Florian, additional, Foroutan, Aidin, additional, Friez, Michael J., additional, Gervasini, Cristina, additional, Haghshenas, Sadegheh, additional, Hilton, Benjamin A., additional, Jenkins, Zandra, additional, Kaur, Simranpreet, additional, Lewis, Suzanne, additional, Louie, Raymond J., additional, Maitz, Silvia, additional, Milani, Donatella, additional, Morgan, Angela T., additional, Oegema, Renske, additional, Østergaard, Elsebet, additional, Pallares, Nathalie R., additional, Piccione, Maria, additional, Plomp, Astrid S., additional, Poulton, Cathryn, additional, Reilly, Jack, additional, Rius, Rocio, additional, Robertson, Stephen, additional, Rooney, Kathleen, additional, Rousseau, Justine, additional, Santen, Gijs W. E., additional, Santos‐Simarro, Fernando, additional, Schijns, Josephine, additional, Squeo, Gabriella M., additional, John, Miya St, additional, Thauvin‐Robinet, Christel, additional, Traficante, Giovanna, additional, van der Sluijs, Pleuntje J., additional, Vergano, Samantha A., additional, Vos, Niels, additional, Walden, Kellie K., additional, Azmanov, Dimitar, additional, Balci, Tugce B., additional, Banka, Siddharth, additional, Gecz, Jozef, additional, Henneman, Peter, additional, Lee, Jennifer A., additional, Mannens, Marcel M. A. M., additional, Roscioli, Tony, additional, Siu, Victoria, additional, Amor, David J., additional, Baynam, Gareth, additional, Bend, Eric G., additional, Boycott, Kym, additional, Brunetti‐Pierri, Nicola, additional, Campeau, Philippe M., additional, Campion, Dominique, additional, Christodoulou, John, additional, Dyment, David, additional, Esber, Natacha, additional, Fahrner, Jill A., additional, Fleming, Mark D., additional, Genevieve, David, additional, Heron, Delphine, additional, Husson, Thomas, additional, Kernohan, Kristin D., additional, McNeill, Alisdair, additional, Menke, Leonie A., additional, Merla, Giuseppe, additional, Prontera, Paolo, additional, Rockman‐Greenberg, Cheryl, additional, Schwartz, Charles, additional, Skinner, Steven A., additional, Stevenson, Roger E., additional, Vincent, Marie, additional, Vitobello, Antonio, additional, Tartaglia, Marco, additional, Alders, Marielle, additional, Tedder, Matthew L., additional, and Sadikovic, Bekim, additional
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- 2022
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13. Discovering a new part of the phenotypic spectrum of Coffin-Siris syndrome in a fetal cohort
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van der Sluijs, Pleuntje J., primary, Joosten, Marieke, additional, Alby, Caroline, additional, Attié-Bitach, Tania, additional, Gilmore, Kelly, additional, Dubourg, Christele, additional, Fradin, Mélanie, additional, Wang, Tianyun, additional, Kurtz-Nelson, Evangeline C., additional, Ahlers, Kaitlyn P., additional, Arts, Peer, additional, Barnett, Christopher P., additional, Ashfaq, Myla, additional, Baban, Anwar, additional, van den Born, Myrthe, additional, Borrie, Sarah, additional, Busa, Tiffany, additional, Byrne, Alicia, additional, Carriero, Miriam, additional, Cesario, Claudia, additional, Chong, Karen, additional, Cueto-González, Anna Maria, additional, Dempsey, Jennifer C., additional, Diderich, Karin E.M., additional, Doherty, Dan, additional, Farholt, Stense, additional, Gerkes, Erica H., additional, Gorokhova, Svetlana, additional, Govaerts, Lutgarde C.P., additional, Gregersen, Pernille A., additional, Hickey, Scott E., additional, Lefebvre, Mathilde, additional, Mari, Francesca, additional, Martinovic, Jelena, additional, Northrup, Hope, additional, O’Leary, Melanie, additional, Parbhoo, Kareesma, additional, Patrier, Sophie, additional, Popp, Bernt, additional, Santos-Simarro, Fernando, additional, Stoltenburg, Corinna, additional, Thauvin-Robinet, Christel, additional, Thompson, Elisabeth, additional, Vulto-van Silfhout, Anneke T., additional, Zahir, Farah R., additional, Scott, Hamish S., additional, Earl, Rachel K., additional, Eichler, Evan E., additional, Vora, Neeta L., additional, Wilnai, Yael, additional, Giordano, Jessica L., additional, Wapner, Ronald J., additional, Rosenfeld, Jill A., additional, Haak, Monique C., additional, and Santen, Gijs W.E., additional
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- 2022
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14. Correction: The ARID1B spectrum in 143 patients: from nonsyndromic intellectual disability to Coffin–Siris syndrome
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van der Sluijs, Pleuntje J., Jansen, Sandra, Vergano, Samantha A., Adachi-Fukuda, Miho, Alanay, Yasemin, AlKindy, Adila, Baban, Anwar, Bayat, Allan, Beck-Wödl, Stefanie, Berry, Katherine, Bijlsma, Emilia K., Bok, Levinus A., Brouwer, Alwin F. J., van der Burgt, Ineke, Campeau, Philippe M., Canham, Natalie, Chrzanowska, Krystyna, Chu, Yoyo W. Y., Chung, Brain H. Y., Dahan, Karin, De Rademaeker, Marjan, Destree, Anne, Dudding-Byth, Tracy, Earl, Rachel, Elcioglu, Nursel, Elias, Ellen R., Fagerberg, Christina, Gardham, Alice, Gener, Blanca, Gerkes, Erica H., Grasshoff, Ute, van Haeringen, Arie, Heitink, Karin R., Herkert, Johanna C., den Hollander, Nicolette S., Horn, Denise, Hunt, David, Kant, Sarina G., Kato, Mitsuhiro, Kayserili, Hülya, Kersseboom, Rogier, Kilic, Esra, Krajewska-Walasek, Malgorzata, Lammers, Kylin, Laulund, Lone W., Lederer, Damien, Lees, Melissa, López-González, Vanesa, Maas, Saskia, Mancini, Grazia M. S., Marcelis, Carlo, Martinez, Francisco, Maystadt, Isabelle, McGuire, Marianne, McKee, Shane, Mehta, Sarju, Metcalfe, Kay, Milunsky, Jeff, Mizuno, Seiji, Moeschler, John B., Netzer, Christian, Ockeloen, Charlotte W., Oehl-Jaschkowitz, Barbara, Okamoto, Nobuhiko, Olminkhof, Sharon N. M., Orellana, Carmen, Pasquier, Laurent, Pottinger, Caroline, Riehmer, Vera, Robertson, Stephen P., Roifman, Maian, Rooryck, Caroline, Ropers, Fabienne G., Rosello, Monica, Ruivenkamp, Claudia A. L., Sagiroglu, Mahmut S., Sallevelt, Suzanne C. E. H., Calvo, Amparo Sanchis, Simsek-Kiper, Pelin O., Soares, Gabriela, Solaeche, Lucia, Sonmez, Fatma Mujgan, Splitt, Miranda, Steenbeek, Duco, Stegmann, Alexander P. A., Stumpel, Constance T. R. M., Tanabe, Saori, Uctepe, Eyyup, Utine, G. Eda, Veenstra-Knol, Hermine E., Venkateswaran, Sunita, Vilain, Catheline, Vincent-Delorme, Catherine, Vulto-van Silfhout, Anneke T., Wheeler, Patricia, Wilson, Golder N., Wilson, Louise C., Wollnik, Bernd, Kosho, Tomoki, Wieczorek, Dagmar, Eichler, Evan, Pfundt, Rolph, de Vries, Bert B. A., Clayton-Smith, Jill, and Santen, Gijs W. E.
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- 2019
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- View/download PDF
15. Novel diagnostic DNA methylation episignatures expand and refine the epigenetic landscapes of Mendelian disorders
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Levy, Michael A., McConkey, Haley, Kerkhof, Jennifer, Barat-Houari, Mouna, Bargiacchi, Sara, Biamino, Elisa, Cappuccio, Gerarda, Ciolfi, Andrea, Clarke, Angus, DuPont, Barbara R., Elting, Mariet W., Faivre, Laurence, Fee, Timothy, Fletcher, Robin S., Cherik, Florian, Foroutan, Aidin, Friez, Michael J., Gervasini, Cristina, Haghshenas, Sadegheh, Hilton, Benjamin A., Jenkins, Zandra, Kaur, Simranpreet, Lewis, Suzanne, Louie, Raymond J., Maitz, Silvia, Milani, Donatella, Morgan, Angela T., Oegema, Renske, Ostergaard, Elsebet, Pallares, Nathalie Ruiz, Piccione, Maria, Pizzi, Simone, Plomp, Astrid S., Poulton, Cathryn, Reilly, Jack, Relator, Raissa, Rius, Rocio, Robertson, Stephen, Rooney, Kathleen, Rousseau, Justine, Santen, Gijs W. E., Santos-Simarro, Fernando, Schijns, Josephine, Squeo, Gabriella Maria, St John, Miya, Thauvin-Robinet, Christel, Traficante, Giovanna, van der Sluijs, Pleuntje J., Vergano, Samantha A., Vos, Niels, Walden, Kellie K., Azmanov, Dimitar, Balci, Tugce, Banka, Siddharth, Gecz, Jozef, Henneman, Peter, Lee, Jennifer A., Mannens, Marcel M. A. M., Roscioli, Tony, Siu, Victoria, Amor, David J., Baynam, Gareth, Bend, Eric G., Boycott, Kym, Brunetti-Pierri, Nicola, Campeau, Philippe M., Christodoulou, John, Dyment, David, Esber, Natacha, Fahrner, Jill A., Fleming, Mark D., Genevieve, David, Kerrnohan, Kristin D., McNeill, Alisdair, Menke, Leonie A., Merla, Giuseppe, Prontera, Paolo, Rockman-Greenberg, Cheryl, Schwartz, Charles, Skinner, Steven A., Stevenson, Roger E., Vitobello, Antonio, Tartaglia, Marco, Alders, Marielle, Tedder, Matthew L., Sadikovic, Bekim, Levy, Michael A., McConkey, Haley, Kerkhof, Jennifer, Barat-Houari, Mouna, Bargiacchi, Sara, Biamino, Elisa, Cappuccio, Gerarda, Ciolfi, Andrea, Clarke, Angus, DuPont, Barbara R., Elting, Mariet W., Faivre, Laurence, Fee, Timothy, Fletcher, Robin S., Cherik, Florian, Foroutan, Aidin, Friez, Michael J., Gervasini, Cristina, Haghshenas, Sadegheh, Hilton, Benjamin A., Jenkins, Zandra, Kaur, Simranpreet, Lewis, Suzanne, Louie, Raymond J., Maitz, Silvia, Milani, Donatella, Morgan, Angela T., Oegema, Renske, Ostergaard, Elsebet, Pallares, Nathalie Ruiz, Piccione, Maria, Pizzi, Simone, Plomp, Astrid S., Poulton, Cathryn, Reilly, Jack, Relator, Raissa, Rius, Rocio, Robertson, Stephen, Rooney, Kathleen, Rousseau, Justine, Santen, Gijs W. E., Santos-Simarro, Fernando, Schijns, Josephine, Squeo, Gabriella Maria, St John, Miya, Thauvin-Robinet, Christel, Traficante, Giovanna, van der Sluijs, Pleuntje J., Vergano, Samantha A., Vos, Niels, Walden, Kellie K., Azmanov, Dimitar, Balci, Tugce, Banka, Siddharth, Gecz, Jozef, Henneman, Peter, Lee, Jennifer A., Mannens, Marcel M. A. M., Roscioli, Tony, Siu, Victoria, Amor, David J., Baynam, Gareth, Bend, Eric G., Boycott, Kym, Brunetti-Pierri, Nicola, Campeau, Philippe M., Christodoulou, John, Dyment, David, Esber, Natacha, Fahrner, Jill A., Fleming, Mark D., Genevieve, David, Kerrnohan, Kristin D., McNeill, Alisdair, Menke, Leonie A., Merla, Giuseppe, Prontera, Paolo, Rockman-Greenberg, Cheryl, Schwartz, Charles, Skinner, Steven A., Stevenson, Roger E., Vitobello, Antonio, Tartaglia, Marco, Alders, Marielle, Tedder, Matthew L., and Sadikovic, Bekim
- Abstract
Overlapping clinical phenotypes and an expanding breadth and complexity of genomic associations are a growing challenge in the diagnosis and clinical management of Mendelian disorders. The functional consequences and clinical impacts of genomic variation may involve unique, disorder-specific, genomic DNA methylation episignatures. In this study, we describe 19 novel episignature disorders and compare the findings alongside 38 previously established episignatures for a total of 57 episignatures associated with 65 genetic syndromes. We demonstrate increasing resolution and specificity ranging from protein complex, gene, sub-gene, protein domain, and even single nucleotide-level Mendelian episignatures. We show the power of multiclass modeling to develop highly accurate and disease-specific diagnostic classifiers. This study significantly expands the number and spectrum of disorders with detectable DNA methylation episignatures, improves the clinical diagnostic capabilities through the resolution of unsolved cases and the reclassification of variants of unknown clinical significance, and provides further insight into the molecular etiology of Mendelian conditions.
- Published
- 2022
16. Functional correlation of genome-wide DNA methylation profiles in genetic neurodevelopmental disorders
- Author
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Levy, Michael A., Relator, Raissa, McConkey, Haley, Pranckeviciene, Erinija, Kerkhof, Jennifer, Barat-Houari, Mouna, Bargiacchi, Sara, Biamino, Elisa, Palomares Bralo, María, Cappuccio, Gerarda, Ciolfi, Andrea, Clarke, Angus, DuPont, Barbara R., Elting, Mariet W., Faivre, Laurence, Fee, Timothy, Ferilli, Marco, Fletcher, Robin S., Cherick, Florian, Foroutan, Aidin, Friez, Michael J., Gervasini, Cristina, Haghshenas, Sadegheh, Hilton, Benjamin A., Jenkins, Zandra, Kaur, Simranpreet, Lewis, Suzanne, Louie, Raymond J., Maitz, Silvia, Milani, Donatella, Morgan, Angela T., Oegema, Renske, Østergaard, Elsebet, Pallares, Nathalie R., Piccione, Maria, Plomp, Astrid S., Poulton, Cathryn, Reilly, Jack, Rius, Rocio, Robertson, Stephen, Rooney, Kathleen, Rousseau, Justine, Santen, Gijs W.E., Santos-Simarro, Fernando, Schijns, Josephine, Squeo, Gabriella M., John, Miya St, Thauvin-Robinet, Christel, Traficante, Giovanna, van der Sluijs, Pleuntje J., Vergano, Samantha A., Vos, Niels, Walden, Kellie K., Azmanov, Dimitar, Balci, Tugce B., Banka, Siddharth, Gecz, Jozef, Henneman, Peter, Lee, Jennifer A., Mannens, Marcel M.A.M., Roscioli, Tony, Siu, Victoria, Amor, David J., Baynam, Gareth, Bend, Eric G., Boycott, Kym, Brunetti-Pierri, Nicola, Campeau, Philippe M., Campion, Dominique, Christodoulou, John, Dyment, David, Esber, Natacha, Fahrner, Jill A., Fleming, Mark D., Genevieve, David, Heron, Delphine, Husson, Thomas, Kernohan, Kristin D., McNeill, Alisdair, Menke, Leonie A., Merla, Giuseppe, Prontera, Paolo, Rockman-Greenberg, Cheryl, Schwartz, Charles, Skinner, Steven A., Stevenson, Roger E., Vincent, Marie, Vitobello, Antonio, Tartaglia, Marco, Alders, Marielle, Tedder, Matthew L., Sadikovic, Bekim, Levy, Michael A., Relator, Raissa, McConkey, Haley, Pranckeviciene, Erinija, Kerkhof, Jennifer, Barat-Houari, Mouna, Bargiacchi, Sara, Biamino, Elisa, Palomares Bralo, María, Cappuccio, Gerarda, Ciolfi, Andrea, Clarke, Angus, DuPont, Barbara R., Elting, Mariet W., Faivre, Laurence, Fee, Timothy, Ferilli, Marco, Fletcher, Robin S., Cherick, Florian, Foroutan, Aidin, Friez, Michael J., Gervasini, Cristina, Haghshenas, Sadegheh, Hilton, Benjamin A., Jenkins, Zandra, Kaur, Simranpreet, Lewis, Suzanne, Louie, Raymond J., Maitz, Silvia, Milani, Donatella, Morgan, Angela T., Oegema, Renske, Østergaard, Elsebet, Pallares, Nathalie R., Piccione, Maria, Plomp, Astrid S., Poulton, Cathryn, Reilly, Jack, Rius, Rocio, Robertson, Stephen, Rooney, Kathleen, Rousseau, Justine, Santen, Gijs W.E., Santos-Simarro, Fernando, Schijns, Josephine, Squeo, Gabriella M., John, Miya St, Thauvin-Robinet, Christel, Traficante, Giovanna, van der Sluijs, Pleuntje J., Vergano, Samantha A., Vos, Niels, Walden, Kellie K., Azmanov, Dimitar, Balci, Tugce B., Banka, Siddharth, Gecz, Jozef, Henneman, Peter, Lee, Jennifer A., Mannens, Marcel M.A.M., Roscioli, Tony, Siu, Victoria, Amor, David J., Baynam, Gareth, Bend, Eric G., Boycott, Kym, Brunetti-Pierri, Nicola, Campeau, Philippe M., Campion, Dominique, Christodoulou, John, Dyment, David, Esber, Natacha, Fahrner, Jill A., Fleming, Mark D., Genevieve, David, Heron, Delphine, Husson, Thomas, Kernohan, Kristin D., McNeill, Alisdair, Menke, Leonie A., Merla, Giuseppe, Prontera, Paolo, Rockman-Greenberg, Cheryl, Schwartz, Charles, Skinner, Steven A., Stevenson, Roger E., Vincent, Marie, Vitobello, Antonio, Tartaglia, Marco, Alders, Marielle, Tedder, Matthew L., and Sadikovic, Bekim
- Abstract
An expanding range of genetic syndromes are characterized by genome-wide disruptions in DNA methylation profiles referred to as episignatures. Episignatures are distinct, highly sensitive, and specific biomarkers that have recently been applied in clinical diagnosis of genetic syndromes. Episignatures are contained within the broader disorder-specific genome-wide DNA methylation changes, which can share significant overlap among different conditions. In this study, we performed functional genomic assessment and comparison of disorder-specific and overlapping genome-wide DNA methylation changes related to 65 genetic syndromes with previously described episignatures. We demonstrate evidence of disorder-specific and recurring genome-wide differentially methylated probes (DMPs) and regions (DMRs). The overall distribution of DMPs and DMRs across the majority of the neurodevelopmental genetic syndromes analyzed showed substantial enrichment in gene promoters and CpG islands, and under-representation of the more variable intergenic regions. Analysis showed significant enrichment of the DMPs and DMRs in gene pathways and processes related to neurodevelopment, including neurogenesis, synaptic signaling and synaptic transmission. This study expands beyond the diagnostic utility of DNA methylation episignatures by demonstrating correlation between the function of the mutated genes and the consequent genomic DNA methylation profiles as a key functional element in the molecular etiology of genetic neurodevelopmental disorders.
- Published
- 2022
17. Functional correlation of genome-wide DNA methylation profiles in genetic neurodevelopmental disorders
- Author
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Genetica Klinische Genetica, Brain, Child Health, Levy, Michael A, Relator, Raissa, McConkey, Haley, Pranckeviciene, Erinija, Kerkhof, Jennifer, Barat-Houari, Mouna, Bargiacchi, Sara, Biamino, Elisa, Bralo, María Palomares, Cappuccio, Gerarda, Ciolfi, Andrea, Clarke, Angus, DuPont, Barbara R, Elting, Mariet W, Faivre, Laurence, Fee, Timothy, Ferilli, Marco, Fletcher, Robin S, Cherick, Florian, Foroutan, Aidin, Friez, Michael J, Gervasini, Cristina, Haghshenas, Sadegheh, Hilton, Benjamin A, Jenkins, Zandra, Kaur, Simranpreet, Lewis, Suzanne, Louie, Raymond J, Maitz, Silvia, Milani, Donatella, Morgan, Angela T, Oegema, Renske, Østergaard, Elsebet, Pallares, Nathalie Ruiz, Piccione, Maria, Plomp, Astrid S, Poulton, Cathryn, Reilly, Jack, Rius, Rocio, Robertson, Stephen, Rooney, Kathleen, Rousseau, Justine, Santen, Gijs W E, Santos-Simarro, Fernando, Schijns, Josephine, Squeo, Gabriella Maria, John, Miya St, Thauvin-Robinet, Christel, Traficante, Giovanna, van der Sluijs, Pleuntje J, Vergano, Samantha A, Vos, Niels, Walden, Kellie K, Azmanov, Dimitar, Balci, Tugce B, Banka, Siddharth, Gecz, Jozef, Henneman, Peter, Lee, Jennifer A, Mannens, Marcel M A M, Roscioli, Tony, Siu, Victoria, Amor, David J, Baynam, Gareth, Bend, Eric G, Boycott, Kym, Brunetti-Pierri, Nicola, Campeau, Philippe M, Campion, Dominique, Christodoulou, John, Dyment, David, Esber, Natacha, Fahrner, Jill A, Fleming, Mark D, Genevieve, David, Heron, Delphine, Husson, Thomas, Kernohan, Kristin D, McNeill, Alisdair, Menke, Leonie A, Merla, Giuseppe, Prontera, Paolo, Rockman-Greenberg, Cheryl, Schwartz, Charles, Skinner, Steven A, Stevenson, Roger E, Vincent, Marie, Vitobello, Antonio, Tartaglia, Marco, Alders, Marielle, Tedder, Matthew L, Sadikovic, Bekim, Genetica Klinische Genetica, Brain, Child Health, Levy, Michael A, Relator, Raissa, McConkey, Haley, Pranckeviciene, Erinija, Kerkhof, Jennifer, Barat-Houari, Mouna, Bargiacchi, Sara, Biamino, Elisa, Bralo, María Palomares, Cappuccio, Gerarda, Ciolfi, Andrea, Clarke, Angus, DuPont, Barbara R, Elting, Mariet W, Faivre, Laurence, Fee, Timothy, Ferilli, Marco, Fletcher, Robin S, Cherick, Florian, Foroutan, Aidin, Friez, Michael J, Gervasini, Cristina, Haghshenas, Sadegheh, Hilton, Benjamin A, Jenkins, Zandra, Kaur, Simranpreet, Lewis, Suzanne, Louie, Raymond J, Maitz, Silvia, Milani, Donatella, Morgan, Angela T, Oegema, Renske, Østergaard, Elsebet, Pallares, Nathalie Ruiz, Piccione, Maria, Plomp, Astrid S, Poulton, Cathryn, Reilly, Jack, Rius, Rocio, Robertson, Stephen, Rooney, Kathleen, Rousseau, Justine, Santen, Gijs W E, Santos-Simarro, Fernando, Schijns, Josephine, Squeo, Gabriella Maria, John, Miya St, Thauvin-Robinet, Christel, Traficante, Giovanna, van der Sluijs, Pleuntje J, Vergano, Samantha A, Vos, Niels, Walden, Kellie K, Azmanov, Dimitar, Balci, Tugce B, Banka, Siddharth, Gecz, Jozef, Henneman, Peter, Lee, Jennifer A, Mannens, Marcel M A M, Roscioli, Tony, Siu, Victoria, Amor, David J, Baynam, Gareth, Bend, Eric G, Boycott, Kym, Brunetti-Pierri, Nicola, Campeau, Philippe M, Campion, Dominique, Christodoulou, John, Dyment, David, Esber, Natacha, Fahrner, Jill A, Fleming, Mark D, Genevieve, David, Heron, Delphine, Husson, Thomas, Kernohan, Kristin D, McNeill, Alisdair, Menke, Leonie A, Merla, Giuseppe, Prontera, Paolo, Rockman-Greenberg, Cheryl, Schwartz, Charles, Skinner, Steven A, Stevenson, Roger E, Vincent, Marie, Vitobello, Antonio, Tartaglia, Marco, Alders, Marielle, Tedder, Matthew L, and Sadikovic, Bekim
- Published
- 2022
18. Novel diagnostic DNA methylation episignatures expand and refine the epigenetic landscapes of Mendelian disorders
- Author
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Levy, Michael A., primary, McConkey, Haley, additional, Kerkhof, Jennifer, additional, Barat-Houari, Mouna, additional, Bargiacchi, Sara, additional, Biamino, Elisa, additional, Bralo, María Palomares, additional, Cappuccio, Gerarda, additional, Ciolfi, Andrea, additional, Clarke, Angus, additional, DuPont, Barbara R., additional, Elting, Mariet W., additional, Faivre, Laurence, additional, Fee, Timothy, additional, Fletcher, Robin S., additional, Cherik, Florian, additional, Foroutan, Aidin, additional, Friez, Michael J., additional, Gervasini, Cristina, additional, Haghshenas, Sadegheh, additional, Hilton, Benjamin A., additional, Jenkins, Zandra, additional, Kaur, Simranpreet, additional, Lewis, Suzanne, additional, Louie, Raymond J., additional, Maitz, Silvia, additional, Milani, Donatella, additional, Morgan, Angela T., additional, Oegema, Renske, additional, Østergaard, Elsebet, additional, Pallares, Nathalie Ruiz, additional, Piccione, Maria, additional, Pizzi, Simone, additional, Plomp, Astrid S., additional, Poulton, Cathryn, additional, Reilly, Jack, additional, Relator, Raissa, additional, Rius, Rocio, additional, Robertson, Stephen, additional, Rooney, Kathleen, additional, Rousseau, Justine, additional, Santen, Gijs W.E., additional, Santos-Simarro, Fernando, additional, Schijns, Josephine, additional, Squeo, Gabriella Maria, additional, St John, Miya, additional, Thauvin-Robinet, Christel, additional, Traficante, Giovanna, additional, van der Sluijs, Pleuntje J., additional, Vergano, Samantha A., additional, Vos, Niels, additional, Walden, Kellie K., additional, Azmanov, Dimitar, additional, Balci, Tugce, additional, Banka, Siddharth, additional, Gecz, Jozef, additional, Henneman, Peter, additional, Lee, Jennifer A., additional, Mannens, Marcel M.A.M., additional, Roscioli, Tony, additional, Siu, Victoria, additional, Amor, David J., additional, Baynam, Gareth, additional, Bend, Eric G., additional, Boycott, Kym, additional, Brunetti-Pierri, Nicola, additional, Campeau, Philippe M., additional, Christodoulou, John, additional, Dyment, David, additional, Esber, Natacha, additional, Fahrner, Jill A., additional, Fleming, Mark D., additional, Genevieve, David, additional, Kerrnohan, Kristin D., additional, McNeill, Alisdair, additional, Menke, Leonie A., additional, Merla, Giuseppe, additional, Prontera, Paolo, additional, Rockman-Greenberg, Cheryl, additional, Schwartz, Charles, additional, Skinner, Steven A., additional, Stevenson, Roger E., additional, Vitobello, Antonio, additional, Tartaglia, Marco, additional, Alders, Marielle, additional, Tedder, Matthew L., additional, and Sadikovic, Bekim, additional
- Published
- 2022
- Full Text
- View/download PDF
19. A Case Series of Familial ARID1B Variants Illustrating Variable Expression and Suggestions to Update the ACMG Criteria
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van der Sluijs, Pleuntje J., primary, Alders, Mariëlle, additional, Dingemans, Alexander J. M., additional, Parbhoo, Kareesma, additional, van Bon, Bregje W., additional, Dempsey, Jennifer C., additional, Doherty, Dan, additional, den Dunnen, Johan T., additional, Gerkes, Erica H., additional, Milller, Ilana M., additional, Moortgat, Stephanie, additional, Regier, Debra S., additional, Ruivenkamp, Claudia A. L., additional, Schmalz, Betsy, additional, Smol, Thomas, additional, Stuurman, Kyra E., additional, Vincent-Delorme, Catherine, additional, de Vries, Bert B. A., additional, Sadikovic, Bekim, additional, Hickey, Scott E., additional, Rosenfeld, Jill A., additional, Maystadt, Isabelle, additional, and Santen, Gijs W. E., additional
- Published
- 2021
- Full Text
- View/download PDF
20. A case series of familial ARID1B variants illustrating variable expression and suggestions to update the ACMG criteria
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van der Sluijs, Pleuntje J., Alders, Mariëlle, Dingemans, Alexander J.M., Parbhoo, Kareesma, van Bon, Bregje W., Dempsey, Jennifer C., Doherty, Dan, Den Dunnen, Johan T., Gerkes, Erica H., Milller, Ilana M., Moortgat, Stephanie, Regier, Debra S., Ruivenkamp, Claudia A.L., Schmalz, Betsy, Smol, Thomas, Stuurman, Kyra E., Vincent-Delorme, Catherine, de Vries, Bert B.A., Sadikovic, Bekim, Hickey, Scott E., Rosenfeld, Jill A., Maystadt, Isabelle, Santen, Gijs W.E., van der Sluijs, Pleuntje J., Alders, Mariëlle, Dingemans, Alexander J.M., Parbhoo, Kareesma, van Bon, Bregje W., Dempsey, Jennifer C., Doherty, Dan, Den Dunnen, Johan T., Gerkes, Erica H., Milller, Ilana M., Moortgat, Stephanie, Regier, Debra S., Ruivenkamp, Claudia A.L., Schmalz, Betsy, Smol, Thomas, Stuurman, Kyra E., Vincent-Delorme, Catherine, de Vries, Bert B.A., Sadikovic, Bekim, Hickey, Scott E., Rosenfeld, Jill A., Maystadt, Isabelle, and Santen, Gijs W.E.
- Abstract
ARID1B is one of the most frequently mutated genes in intellectual disability (~1%). Most variants are readily classified, since they are de novo and are predicted to lead to loss of function, and therefore classified as pathogenic according to the American College of Medical Genetics and Genomics (ACMG) guidelines for the interpretation of sequence variants. However, familial loss-of-function variants can also occur and can be challenging to interpret. Such variants may be pathogenic with variable expression, causing only a mild phenotype in a parent. Alternatively, since some regions of the ARID1B gene seem to be lacking pathogenic variants, loss-of-function variants in those regions may not lead to ARID1B haploinsufficiency and may therefore be benign. We describe 12 families with potential loss-of-function variants, which were either familial or with unknown inheritance and were in regions where pathogenic variants have not been described or are otherwise challenging to interpret. We performed detailed clinical and DNA methylation studies, which allowed us to confidently classify most variants. In five families we observed transmission of pathogenic variants, confirming their highly variable expression. Our findings provide further evidence for an alternative translational start site and we suggest updates for the ACMG guidelines for the interpretation of sequence variants to incorporate DNA methylation studies and facial analyses.
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- 2021
21. Correction: Putting genome-wide sequencing in neonates into perspective
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Genetica Klinische Genetica, Cancer, van der Sluijs, Pleuntje J., Aten, Emmelien, Barge-Schaapveld, Daniela Q.C.M., Bijlsma, Emilia K., Bökenkamp-Gramann, Regina, Kaat, Laura Donker, van Doorn, Remco, van de Putte, Dietje Fransen, van Haeringen, Arie, ten Harkel, Arend D.J., Hilhorst-Hofstee, Yvonne, Hoffer, Mariette J.V., den Hollander, Nicolette S., van Ierland, Yvette, Koopmans, Marije, Kriek, Marjolein, Moghadasi, Setareh, Nibbeling, Esther A.R., Peeters-Scholte, Cacha M.P.C.D., Potjer, Thomas P., van Rij, Maartje, Ruivenkamp, Claudia A.L., Rutten, Julie W., Steggerda, Sylke J., Suerink, Manon, Tan, Ratna N.G.B., van der Tuin, Karin, Visser, Remco, van der Werf–t Lam, Anne Sophie, Williams, Monique, Witlox, Ruben, Santen, Gijs W.E., Genetica Klinische Genetica, Cancer, van der Sluijs, Pleuntje J., Aten, Emmelien, Barge-Schaapveld, Daniela Q.C.M., Bijlsma, Emilia K., Bökenkamp-Gramann, Regina, Kaat, Laura Donker, van Doorn, Remco, van de Putte, Dietje Fransen, van Haeringen, Arie, ten Harkel, Arend D.J., Hilhorst-Hofstee, Yvonne, Hoffer, Mariette J.V., den Hollander, Nicolette S., van Ierland, Yvette, Koopmans, Marije, Kriek, Marjolein, Moghadasi, Setareh, Nibbeling, Esther A.R., Peeters-Scholte, Cacha M.P.C.D., Potjer, Thomas P., van Rij, Maartje, Ruivenkamp, Claudia A.L., Rutten, Julie W., Steggerda, Sylke J., Suerink, Manon, Tan, Ratna N.G.B., van der Tuin, Karin, Visser, Remco, van der Werf–t Lam, Anne Sophie, Williams, Monique, Witlox, Ruben, and Santen, Gijs W.E.
- Published
- 2019
22. The ARID1B spectrum in 143 patients: from nonsyndromic intellectual disability to Coffin–Siris syndrome
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Karabey, Hülya Kayserili (ORCID 0000-0003-0376-499X & YÖK ID 7945), van der Sluijs, Pleuntje J.; Jansen, Sandra; Vergano, Samantha A.; Adachi-Fukuda, Miho; Alanay, Yasemin; AlKindy, Adila; Baban, Anwar; Bayat, Allan; Beck-Woedl, Stefanie; Berry, Katherine; Bijlsma, Emilia K.; Bok, Levinus A.; Brouwer, Alwin F. J.; van der Burgt, Ineke; Campeau, Philippe M.; Canham, Natalie; Chrzanowska, Krystyna; Chu, Yoyo W. Y.; Chung, Brain H. Y.; Dahan, Karin; De Rademaeker, Marjan; Destree, Anne; Dudding-Byth, Tracy; Earl, Rachel; Elçioğlu, Nursel; Elias, Ellen R.; Fagerberg, Christina; Gardham, Alice; Gener, Blanca; Gerkes, Erica H.; Grasshoff, Ute; van Haeringen, Arie; Heitink, Karin R.; Herkert, Johanna C.; den Hollander, Nicolette S.; Horn, Denise; Hunt, David; Kant, Sarina G.; Kato, Mitsuhiro; Kersseboom, Rogier; Kılıç, Esra; Krajewska-Walasek, Malgorzata; Lammers, Kylin; Laulund, Lone W.; Lederer, Damien; Lees, Melissa; Lopez-Gonzalez, Vanesa; Maas, Saskia; Mancini, Grazia M. S.; Marcelis, Carlo; Martinez, Francisco; Maystadt, Isabelle; McGuire, Marianne; McKee, Shane; Mehta, Sarju; Metcalfe, Kay; Milunsky, Jeff; Mizuno, Seiji; Moeschler, John B.; Netzer, Christian; Ockeloen, Charlotte W.; Oehl-Jaschkowitz, Barbara; Okamoto, Nobuhiko; Olminkhof, Sharon N. M.; Orellana, Carmen; Pasquier, Laurent; Pottinger, Caroline; Riehmer, Vera; Robertson, Stephen P.; Roifman, Maian; Rooryck, Caroline; Ropers, Fabienne G.; Rosello, Monica; Ruivenkamp, Claudia A. L.; Sağıroğlu, Mahmut S.; Sallevelt, Suzanne C. E. H.; Sanchis Calvo, Amparo; Şimşek-Kiper, Pelin O.; Soares, Gabriela; Solaeche, Lucia; Sönmez, Fatma Müjgan; Splitt, Miranda; Steenbeek, Duco; Stegmann, Alexander P. A.; Stumpel, Constance T. R. M.; Tanabe, Saori; Üçtepe, Eyyüp; Utine, G. Eda; Veenstra-Knol, Hermine E.; Venkateswaran, Sunita; Vilain, Catheline; Vincent-Delorme, Catherine; Vulto-van Silfhout, Anneke T.; Wheeler, Patricia; Wilson, Golder N.; Wilson, Louise C.; Wollnik, Bernd; Kosho, Tomoki; Wieczorek, Dagmar; Eichler, Evan; Pfundt, Rolph; de Vries, Bert B. A.; Clayton-Smith, Jill; S, School of Medicine, Department of Medical Genetics, Karabey, Hülya Kayserili (ORCID 0000-0003-0376-499X & YÖK ID 7945), van der Sluijs, Pleuntje J.; Jansen, Sandra; Vergano, Samantha A.; Adachi-Fukuda, Miho; Alanay, Yasemin; AlKindy, Adila; Baban, Anwar; Bayat, Allan; Beck-Woedl, Stefanie; Berry, Katherine; Bijlsma, Emilia K.; Bok, Levinus A.; Brouwer, Alwin F. J.; van der Burgt, Ineke; Campeau, Philippe M.; Canham, Natalie; Chrzanowska, Krystyna; Chu, Yoyo W. Y.; Chung, Brain H. Y.; Dahan, Karin; De Rademaeker, Marjan; Destree, Anne; Dudding-Byth, Tracy; Earl, Rachel; Elçioğlu, Nursel; Elias, Ellen R.; Fagerberg, Christina; Gardham, Alice; Gener, Blanca; Gerkes, Erica H.; Grasshoff, Ute; van Haeringen, Arie; Heitink, Karin R.; Herkert, Johanna C.; den Hollander, Nicolette S.; Horn, Denise; Hunt, David; Kant, Sarina G.; Kato, Mitsuhiro; Kersseboom, Rogier; Kılıç, Esra; Krajewska-Walasek, Malgorzata; Lammers, Kylin; Laulund, Lone W.; Lederer, Damien; Lees, Melissa; Lopez-Gonzalez, Vanesa; Maas, Saskia; Mancini, Grazia M. S.; Marcelis, Carlo; Martinez, Francisco; Maystadt, Isabelle; McGuire, Marianne; McKee, Shane; Mehta, Sarju; Metcalfe, Kay; Milunsky, Jeff; Mizuno, Seiji; Moeschler, John B.; Netzer, Christian; Ockeloen, Charlotte W.; Oehl-Jaschkowitz, Barbara; Okamoto, Nobuhiko; Olminkhof, Sharon N. M.; Orellana, Carmen; Pasquier, Laurent; Pottinger, Caroline; Riehmer, Vera; Robertson, Stephen P.; Roifman, Maian; Rooryck, Caroline; Ropers, Fabienne G.; Rosello, Monica; Ruivenkamp, Claudia A. L.; Sağıroğlu, Mahmut S.; Sallevelt, Suzanne C. E. H.; Sanchis Calvo, Amparo; Şimşek-Kiper, Pelin O.; Soares, Gabriela; Solaeche, Lucia; Sönmez, Fatma Müjgan; Splitt, Miranda; Steenbeek, Duco; Stegmann, Alexander P. A.; Stumpel, Constance T. R. M.; Tanabe, Saori; Üçtepe, Eyyüp; Utine, G. Eda; Veenstra-Knol, Hermine E.; Venkateswaran, Sunita; Vilain, Catheline; Vincent-Delorme, Catherine; Vulto-van Silfhout, Anneke T.; Wheeler, Patricia; Wilson, Golder N.; Wilson, Louise C.; Wollnik, Bernd; Kosho, Tomoki; Wieczorek, Dagmar; Eichler, Evan; Pfundt, Rolph; de Vries, Bert B. A.; Clayton-Smith, Jill; S, School of Medicine, and Department of Medical Genetics
- Abstract
Purpose: pathogenic variants in ARID1B are one of the most frequent causes of intellectual disability (ID) as determined by large-scale exome sequencing studies. Most studies published thus far describe clinically diagnosed Coffin–Siris patients (ARID1B-CSS) and it is unclear whether these data are representative for patients identified through sequencing of unbiased ID cohorts (ARID1B-ID). We therefore sought to determine genotypic and phenotypic differences between ARID1B-ID and ARID1B-CSS. In parallel, we investigated the effect of different methods of phenotype reporting. Methods: clinicians entered clinical data in an extensive web-based survey. Results: 79 ARID1B-CSS and 64 ARID1B-ID patients were included. CSS-associated dysmorphic features, such as thick eyebrows, long eyelashes, thick alae nasi, long and/or broad philtrum, small nails and small or absent fifth distal phalanx and hypertrichosis, were observed significantly more often (p < 0.001) in ARID1B-CSS patients. No other significant differences were identified. Conclusion: there are only minor differences between ARID1B-ID and ARID1B-CSS patients. ARID1B-related disorders seem to consist of a spectrum, and patients should be managed similarly. We demonstrated that data collection methods without an explicit option to report the absence of a feature (such as most Human Phenotype Ontology-based methods) tended to underestimate gene-related features., Netherlands Organisation for Health Research and Development
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- 2019
23. The ARID1B spectrum in 143 patients:from nonsyndromic intellectual disability to Coffin–Siris syndrome
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van der Sluijs, Pleuntje J., Jansen, Sandra, Vergano, Samantha A., Adachi-Fukuda, Miho, Alanay, Yasemin, AlKindy, Adila, Baban, Anwar, Bayat, Allan, Beck-Wödl, Stefanie, Berry, Katherine, Bijlsma, Emilia K., Bok, Levinus A., Brouwer, Alwin F.J., van der Burgt, Ineke, Campeau, Philippe M., Canham, Natalie, Chrzanowska, Krystyna, Chu, Yoyo W.Y., Chung, Brain H.Y., Dahan, Karin, De Rademaeker, Marjan, Destree, Anne, Dudding-Byth, Tracy, Earl, Rachel, Elcioglu, Nursel, Elias, Ellen R., Fagerberg, Christina, Gardham, Alice, Gener, Blanca, Gerkes, Erica H., Grasshoff, Ute, van Haeringen, Arie, Heitink, Karin R., Herkert, Johanna C., den Hollander, Nicolette S., Horn, Denise, Hunt, David, Kant, Sarina G., Kato, Mitsuhiro, Kayserili, Hülya, Kersseboom, Rogier, Kilic, Esra, Krajewska-Walasek, Malgorzata, Lammers, Kylin, Laulund, Lone W., Lederer, Damien, Lees, Melissa, López-González, Vanesa, Maas, Saskia, Mancini, Grazia M.S., van der Sluijs, Pleuntje J., Jansen, Sandra, Vergano, Samantha A., Adachi-Fukuda, Miho, Alanay, Yasemin, AlKindy, Adila, Baban, Anwar, Bayat, Allan, Beck-Wödl, Stefanie, Berry, Katherine, Bijlsma, Emilia K., Bok, Levinus A., Brouwer, Alwin F.J., van der Burgt, Ineke, Campeau, Philippe M., Canham, Natalie, Chrzanowska, Krystyna, Chu, Yoyo W.Y., Chung, Brain H.Y., Dahan, Karin, De Rademaeker, Marjan, Destree, Anne, Dudding-Byth, Tracy, Earl, Rachel, Elcioglu, Nursel, Elias, Ellen R., Fagerberg, Christina, Gardham, Alice, Gener, Blanca, Gerkes, Erica H., Grasshoff, Ute, van Haeringen, Arie, Heitink, Karin R., Herkert, Johanna C., den Hollander, Nicolette S., Horn, Denise, Hunt, David, Kant, Sarina G., Kato, Mitsuhiro, Kayserili, Hülya, Kersseboom, Rogier, Kilic, Esra, Krajewska-Walasek, Malgorzata, Lammers, Kylin, Laulund, Lone W., Lederer, Damien, Lees, Melissa, López-González, Vanesa, Maas, Saskia, and Mancini, Grazia M.S.
- Abstract
Purpose: Pathogenic variants in ARID1B are one of the most frequent causes of intellectual disability (ID) as determined by large-scale exome sequencing studies. Most studies published thus far describe clinically diagnosed Coffin–Siris patients (ARID1B-CSS) and it is unclear whether these data are representative for patients identified through sequencing of unbiased ID cohorts (ARID1B-ID). We therefore sought to determine genotypic and phenotypic differences between ARID1B-ID and ARID1B-CSS. In parallel, we investigated the effect of different methods of phenotype reporting. Methods: Clinicians entered clinical data in an extensive web-based survey. Results: 79 ARID1B-CSS and 64 ARID1B-ID patients were included. CSS-associated dysmorphic features, such as thick eyebrows, long eyelashes, thick alae nasi, long and/or broad philtrum, small nails and small or absent fifth distal phalanx and hypertrichosis, were observed significantly more often (p < 0.001) in ARID1B-CSS patients. No other significant differences were identified. Conclusion: There are only minor differences between ARID1B-ID and ARID1B-CSS patients. ARID1B-related disorders seem to consist of a spectrum, and patients should be managed similarly. We demonstrated that data collection methods without an explicit option to report the absence of a feature (such as most Human Phenotype Ontology-based methods) tended to underestimate gene-related features.
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- 2019
24. Correction:The ARID1B spectrum in 143 patients: from nonsyndromic intellectual disability to Coffin–Siris syndrome (Genetics in Medicine, (2019), 21, 6, (1295-1307), 10.1038/s41436-018-0330-z)
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van der Sluijs, Pleuntje J., Jansen, Sandra, Vergano, Samantha A., Adachi-Fukuda, Miho, Alanay, Yasemin, AlKindy, Adila, Baban, Anwar, Bayat, Allan, Beck-Wödl, Stefanie, Berry, Katherine, Bijlsma, Emilia K., Bok, Levinus A., Brouwer, Alwin F.J., van der Burgt, Ineke, Campeau, Philippe M., Canham, Natalie, Chrzanowska, Krystyna, Chu, Yoyo W.Y., Chung, Brain H.Y., Dahan, Karin, De Rademaeker, Marjan, Destree, Anne, Dudding-Byth, Tracy, Earl, Rachel, Elcioglu, Nursel, Elias, Ellen R., Fagerberg, Christina, Gardham, Alice, Gener, Blanca, Gerkes, Erica H., Grasshoff, Ute, van Haeringen, Arie, Heitink, Karin R., Herkert, Johanna C., den Hollander, Nicolette S., Horn, Denise, Hunt, David, Kant, Sarina G., Kato, Mitsuhiro, Kayserili, Hülya, Kersseboom, Rogier, Kilic, Esra, Krajewska-Walasek, Malgorzata, Lammers, Kylin, Laulund, Lone W., Lederer, Damien, Lees, Melissa, López-González, Vanesa, Maas, Saskia, Mancini, Grazia M.S., van der Sluijs, Pleuntje J., Jansen, Sandra, Vergano, Samantha A., Adachi-Fukuda, Miho, Alanay, Yasemin, AlKindy, Adila, Baban, Anwar, Bayat, Allan, Beck-Wödl, Stefanie, Berry, Katherine, Bijlsma, Emilia K., Bok, Levinus A., Brouwer, Alwin F.J., van der Burgt, Ineke, Campeau, Philippe M., Canham, Natalie, Chrzanowska, Krystyna, Chu, Yoyo W.Y., Chung, Brain H.Y., Dahan, Karin, De Rademaeker, Marjan, Destree, Anne, Dudding-Byth, Tracy, Earl, Rachel, Elcioglu, Nursel, Elias, Ellen R., Fagerberg, Christina, Gardham, Alice, Gener, Blanca, Gerkes, Erica H., Grasshoff, Ute, van Haeringen, Arie, Heitink, Karin R., Herkert, Johanna C., den Hollander, Nicolette S., Horn, Denise, Hunt, David, Kant, Sarina G., Kato, Mitsuhiro, Kayserili, Hülya, Kersseboom, Rogier, Kilic, Esra, Krajewska-Walasek, Malgorzata, Lammers, Kylin, Laulund, Lone W., Lederer, Damien, Lees, Melissa, López-González, Vanesa, Maas, Saskia, and Mancini, Grazia M.S.
- Abstract
The original version of this Article contained an error in the spelling of the author Pleuntje J. van der Sluijs, which was incorrectly given as Eline (P. J.) van der Sluijs. This has now been corrected in both the PDF and HTML versions of the Article.
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- 2019
25. Microduplications of ARID1Aand ARID1Bcause a novel clinical and epigenetic distinct BAFopathy
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van der Sluijs, Pleuntje J., Moutton, Sébastien, Dingemans, Alexander J.M., Weis, Denisa, Levy, Michael A., Boycott, Kym M., Arberas, Claudia, Baldassarri, Margherita, Beneteau, Claire, Brusco, Alfredo, Coutton, Charles, Dabir, Tabib, Dentici, Maria L., Devriendt, Koenraad, Faivre, Laurence, van Haelst, Mieke M., Jizi, Khadije, Kempers, Marlies J., Kerkhof, Jennifer, Kharbanda, Mira, Lachlan, Katherine, Marle, Nathalie, McConkey, Haley, Mencarelli, Maria A., Mowat, David., Niceta, Marcello, Nicolas, Claire, Novelli, Antonio, Orlando, Valeria, Pichon, Olivier, Rankin, Julia, Relator, Raissa., Ropers, Fabienne G., Rosenfeld, Jill A., Sachdev, Rani, Sandaradura, Sarah A., Shukarova-Angelovska, Elena, Steenbeek, Duco, Tartaglia, Marco, Tedder, Matthew A., Trajkova, Slavica, Winer, Norbert, Woods, Jeremy, de Vries, Bert B.A., Sadikovic, Bekim, Alders, Marielle, and Santen, Gijs W.E.
- Abstract
ARID1A/ARID1Bhaploinsufficiency leads to Coffin-Siris syndrome, duplications of ARID1Alead to a distinct clinical syndrome, whilst ARID1Bduplications have not yet been linked to a phenotype.
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- 2024
- Full Text
- View/download PDF
26. Discovering a new part of the phenotypic spectrum of Coffin-Siris syndrome in a fetal cohort
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Pleuntje J. van der Sluijs, Marieke Joosten, Caroline Alby, Tania Attié-Bitach, Kelly Gilmore, Christele Dubourg, Mélanie Fradin, Tianyun Wang, Evangeline C. Kurtz-Nelson, Kaitlyn P. Ahlers, Peer Arts, Christopher P. Barnett, Myla Ashfaq, Anwar Baban, Myrthe van den Born, Sarah Borrie, Tiffany Busa, Alicia Byrne, Miriam Carriero, Claudia Cesario, Karen Chong, Anna Maria Cueto-González, Jennifer C. Dempsey, Karin E.M. Diderich, Dan Doherty, Stense Farholt, Erica H. Gerkes, Svetlana Gorokhova, Lutgarde C.P. Govaerts, Pernille A. Gregersen, Scott E. Hickey, Mathilde Lefebvre, Francesca Mari, Jelena Martinovic, Hope Northrup, Melanie O’Leary, Kareesma Parbhoo, Sophie Patrier, Bernt Popp, Fernando Santos-Simarro, Corinna Stoltenburg, Christel Thauvin-Robinet, Elisabeth Thompson, Anneke T. Vulto-van Silfhout, Farah R. Zahir, Hamish S. Scott, Rachel K. Earl, Evan E. Eichler, Neeta L. Vora, Yael Wilnai, Jessica L. Giordano, Ronald J. Wapner, Jill A. Rosenfeld, Monique C. Haak, Gijs W.E. Santen, Leiden University Medical Center (LUMC), Universiteit Leiden, Erasmus University Medical Center [Rotterdam] (Erasmus MC), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC), Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), CHU Pontchaillou [Rennes], Hôpital de la Timone [CHU - APHM] (TIMONE), Marseille medical genetics - Centre de génétique médicale de Marseille (MMG), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Agro Dijon, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), CHU Rouen, Normandie Université (NU), Columbia University Medical Center (CUMC), Columbia University [New York], Baylor College of Medicine (BCM), Baylor University, This work was supported, in part, by grants from the National Institutes of Health (Grant No. R01 MH101221 [to E.E.E.]). E.E.E. is an investigator of the Howard Hughes Medical Institute.Sequencing and analysis for individual 30 was provided by the Broad Institute of MIT and Harvard Center for Mendelian Genomics and was funded by the National Human Genome Research Institute, the National Eye Institute, and the National Heart, Lung, and Blood Institute (Grant Nos. UM1 HG008900 and R01 HG009141).Sequencing and analysis of cases 5 and 18 was funded by the National Institute of Child Human Development (Grant Nos. K23 HD088742 and R01 HD105868 [to N.L.V.])., Emergency Medicine, Clinical Genetics, van der Sluijs, Pleuntje J, Joosten, Marieke, Alby, Caroline, Attié-Bitach, Tania, Arts, Peer, Byrne, Alicia, Scott, Hamish S, and Santen, Gijs WE
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prenatal ,genetic association ,Chromosomal Proteins, Non-Histone ,Micrognathism ,SMARCB1 ,genetic vulnerability ,Article ,Fetal ,SMARCA4 ,Intellectual Disability ,Humans ,Coffin-Siris syndrome ,Abnormalities, Multiple ,Genetic Association Studies ,Genetics (clinical) ,Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7] ,BAF-complex ,SMARCB ,ARID1A ,ARID1B BAFopathy ,Phenotype ,[SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics ,Face ,abnormalities ,Hand Deformities, Congenital ,Neck - Abstract
Purpose: Genome-wide sequencing is increasingly being performed during pregnancy to identify the genetic cause of congenital anomalies. The interpretation of prenatally identified variants can be challenging and is hampered by our often limited knowledge of prenatal phenotypes. To better delineate the prenatal phenotype of Coffin-Siris syndrome (CSS), we collected clinical data from patients with a prenatal phenotype and a pathogenic variant in one of the CSS-associated genes. Methods: Clinical data was collected through an extensive web-based survey. Results: We included 44 patients with a variant in a CSS-associated gene and a prenatal phenotype; 9 of these patients have been reported before. Prenatal anomalies that were frequently observed in our cohort include hydrocephalus, agenesis of the corpus callosum, hypoplastic left heart syndrome, persistent left vena cava, diaphragmatic hernia, renal agenesis, and intrauterine growth restriction. Anal anomalies were frequently identified after birth in patients with ARID1A variants (6/14, 43%). Interestingly, pathogenic ARID1A variants were much more frequently identified in the current prenatal cohort (16/44, 36%) than in postnatal CSS cohorts (5%-9%). Conclusion: Our data shed new light on the prenatal phenotype of patients with pathogenic variants in CSS genes. (C) 2022 American College of Medical Genetics and Genomics. Published by Elsevier Inc. All rights reserved.
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- 2022
27. Functional correlation of genome-wide DNA methylation profiles in genetic neurodevelopmental disorders
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Michael A. Levy, Raissa Relator, Haley McConkey, Erinija Pranckeviciene, Jennifer Kerkhof, Mouna Barat‐Houari, Sara Bargiacchi, Elisa Biamino, María Palomares Bralo, Gerarda Cappuccio, Andrea Ciolfi, Angus Clarke, Barbara R. DuPont, Mariet W. Elting, Laurence Faivre, Timothy Fee, Marco Ferilli, Robin S. Fletcher, Florian Cherick, Aidin Foroutan, Michael J. Friez, Cristina Gervasini, Sadegheh Haghshenas, Benjamin A. Hilton, Zandra Jenkins, Simranpreet Kaur, Suzanne Lewis, Raymond J. Louie, Silvia Maitz, Donatella Milani, Angela T. Morgan, Renske Oegema, Elsebet Østergaard, Nathalie R. Pallares, Maria Piccione, Astrid S. Plomp, Cathryn Poulton, Jack Reilly, Rocio Rius, Stephen Robertson, Kathleen Rooney, Justine Rousseau, Gijs W. E. Santen, Fernando Santos‐Simarro, Josephine Schijns, Gabriella M. Squeo, Miya St John, Christel Thauvin‐Robinet, Giovanna Traficante, Pleuntje J. van der Sluijs, Samantha A. Vergano, Niels Vos, Kellie K. Walden, Dimitar Azmanov, Tugce B. Balci, Siddharth Banka, Jozef Gecz, Peter Henneman, Jennifer A. Lee, Marcel M. A. M. Mannens, Tony Roscioli, Victoria Siu, David J. Amor, Gareth Baynam, Eric G. Bend, Kym Boycott, Nicola Brunetti‐Pierri, Philippe M. Campeau, Dominique Campion, John Christodoulou, David Dyment, Natacha Esber, Jill A. Fahrner, Mark D. Fleming, David Genevieve, Delphine Heron, Thomas Husson, Kristin D. Kernohan, Alisdair McNeill, Leonie A. Menke, Giuseppe Merla, Paolo Prontera, Cheryl Rockman‐Greenberg, Charles Schwartz, Steven A. Skinner, Roger E. Stevenson, Marie Vincent, Antonio Vitobello, Marco Tartaglia, Marielle Alders, Matthew L. Tedder, Bekim Sadikovic, Human genetics, Amsterdam Reproduction & Development (AR&D), Pediatrics, Levy M.A., Relator R., McConkey H., Pranckeviciene E., Kerkhof J., Barat-Houari M., Bargiacchi S., Biamino E., Palomares Bralo M., Cappuccio G., Ciolfi A., Clarke A., DuPont B.R., Elting M.W., Faivre L., Fee T., Ferilli M., Fletcher R.S., Cherick F., Foroutan A., Friez M.J., Gervasini C., Haghshenas S., Hilton B.A., Jenkins Z., Kaur S., Lewis S., Louie R.J., Maitz S., Milani D., Morgan A.T., Oegema R., Ostergaard E., Pallares N.R., Piccione M., Plomp A.S., Poulton C., Reilly J., Rius R., Robertson S., Rooney K., Rousseau J., Santen G.W.E., Santos-Simarro F., Schijns J., Squeo G.M., John M.S., Thauvin-Robinet C., Traficante G., van der Sluijs P.J., Vergano S.A., Vos N., Walden K.K., Azmanov D., Balci T.B., Banka S., Gecz J., Henneman P., Lee J.A., Mannens M.M.A.M., Roscioli T., Siu V., Amor D.J., Baynam G., Bend E.G., Boycott K., Brunetti-Pierri N., Campeau P.M., Campion D., Christodoulou J., Dyment D., Esber N., Fahrner J.A., Fleming M.D., Genevieve D., Heron D., Husson T., Kernohan K.D., McNeill A., Menke L.A., Merla G., Prontera P., Rockman-Greenberg C., Schwartz C., Skinner S.A., Stevenson R.E., Vincent M., Vitobello A., Tartaglia M., Alders M., Tedder M.L., Sadikovic B., Levy, Michael A, Relator, Raissa, Mcconkey, Haley, Pranckeviciene, Erinija, Kerkhof, Jennifer, Barat-Houari, Mouna, Bargiacchi, Sara, Biamino, Elisa, Bralo, María Palomare, Cappuccio, Gerarda, Ciolfi, Andrea, Clarke, Angu, Dupont, Barbara R, Elting, Mariet W, Faivre, Laurence, Fee, Timothy, Ferilli, Marco, Fletcher, Robin S, Cherick, Florian, Foroutan, Aidin, Friez, Michael J, Gervasini, Cristina, Haghshenas, Sadegheh, Hilton, Benjamin A, Jenkins, Zandra, Kaur, Simranpreet, Lewis, Suzanne, Louie, Raymond J, Maitz, Silvia, Milani, Donatella, Morgan, Angela T, Oegema, Renske, Østergaard, Elsebet, Pallares, Nathalie Ruiz, Piccione, Maria, Plomp, Astrid S, Poulton, Cathryn, Reilly, Jack, Rius, Rocio, Robertson, Stephen, Rooney, Kathleen, Rousseau, Justine, Santen, Gijs W E, Santos-Simarro, Fernando, Schijns, Josephine, Squeo, Gabriella Maria, John, Miya St, Thauvin-Robinet, Christel, Traficante, Giovanna, van der Sluijs, Pleuntje J, Vergano, Samantha A, Vos, Niel, Walden, Kellie K, Azmanov, Dimitar, Balci, Tugce B, Banka, Siddharth, Gecz, Jozef, Henneman, Peter, Lee, Jennifer A, Mannens, Marcel M A M, Roscioli, Tony, Siu, Victoria, Amor, David J, Baynam, Gareth, Bend, Eric G, Boycott, Kym, Brunetti-Pierri, Nicola, Campeau, Philippe M, Campion, Dominique, Christodoulou, John, Dyment, David, Esber, Natacha, Fahrner, Jill A, Fleming, Mark D, Genevieve, David, Heron, Delphine, Husson, Thoma, Kernohan, Kristin D, Mcneill, Alisdair, Menke, Leonie A, Merla, Giuseppe, Prontera, Paolo, Rockman-Greenberg, Cheryl, Schwartz, Charle, Skinner, Steven A, Stevenson, Roger E, Vincent, Marie, Vitobello, Antonio, Tartaglia, Marco, Alders, Marielle, Tedder, Matthew L, Sadikovic, Bekim, Human Genetics, General Paediatrics, Graduate School, AGEM - Amsterdam Gastroenterology Endocrinology Metabolism, ARD - Amsterdam Reproduction and Development, ANS - Cellular & Molecular Mechanisms, ANS - Complex Trait Genetics, and ACS - Pulmonary hypertension & thrombosis
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DNA methylation ,clinical diagnostics ,Syndrome ,DNA methylation, clinical diagnostics, episignatures, neurodevelopmental syndromes ,neurodevelopmental syndromes ,Epigenesis, Genetic ,Neurodevelopmental Disorders ,Genetics ,Humans ,CpG Islands ,DNA, Intergenic ,episignatures ,Episignature ,Genetics (clinical) - Abstract
An expanding range of genetic syndromes are characterized by genome-wide disruptions in DNA methylation profiles referred to as episignatures. Episignatures are distinct, highly sensitive and specific biomarkers that have recently been applied in clinical diagnosis of genetic syndromes. Episignatures are contained within the broader disorder-specific genome-wide DNA methylation changes which can share significant overlap amongst different conditions. In this study we performed functional genomic assessment and comparison of disorder-specific and overlapping genome-wide DNA methylation changes related to 65 genetic syndromes with previously described episignatures. We demonstrate evidence of disorder-specific and recurring genome-wide differentially methylated probes (DMPs) and regions (DMRs). The overall distribution of DMPs and DMRs across the majority of the neurodevelopmental genetic syndromes analyzed showed substantial enrichment in gene promoters and CpG islands, and under-representation of the more variable intergenic regions. Analysis showed significant enrichment of the DMPs and DMRs in gene pathways and processes related to neurodevelopment, including neurogenesis, synaptic signaling and synaptic transmission. This study expands beyond the diagnostic utility of DNA methylation episignatures by demonstrating correlation between the function of the mutated genes and the consequent genomic DNA methylation profiles as a key functional element in the molecular etiology of genetic neurodevelopmental disorders. This article is protected by copyright. All rights reserved.
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- 2022
28. Novel diagnostic DNA methylation episignatures expand and refine the epigenetic landscapes of Mendelian disorders
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Michael A. Levy, Haley McConkey, Jennifer Kerkhof, Mouna Barat-Houari, Sara Bargiacchi, Elisa Biamino, María Palomares Bralo, Gerarda Cappuccio, Andrea Ciolfi, Angus Clarke, Barbara R. DuPont, Mariet W. Elting, Laurence Faivre, Timothy Fee, Robin S. Fletcher, Florian Cherik, Aidin Foroutan, Michael J. Friez, Cristina Gervasini, Sadegheh Haghshenas, Benjamin A. Hilton, Zandra Jenkins, Simranpreet Kaur, Suzanne Lewis, Raymond J. Louie, Silvia Maitz, Donatella Milani, Angela T. Morgan, Renske Oegema, Elsebet Østergaard, Nathalie Ruiz Pallares, Maria Piccione, Simone Pizzi, Astrid S. Plomp, Cathryn Poulton, Jack Reilly, Raissa Relator, Rocio Rius, Stephen Robertson, Kathleen Rooney, Justine Rousseau, Gijs W.E. Santen, Fernando Santos-Simarro, Josephine Schijns, Gabriella Maria Squeo, Miya St John, Christel Thauvin-Robinet, Giovanna Traficante, Pleuntje J. van der Sluijs, Samantha A. Vergano, Niels Vos, Kellie K. Walden, Dimitar Azmanov, Tugce Balci, Siddharth Banka, Jozef Gecz, Peter Henneman, Jennifer A. Lee, Marcel M.A.M. Mannens, Tony Roscioli, Victoria Siu, David J. Amor, Gareth Baynam, Eric G. Bend, Kym Boycott, Nicola Brunetti-Pierri, Philippe M. Campeau, John Christodoulou, David Dyment, Natacha Esber, Jill A. Fahrner, Mark D. Fleming, David Genevieve, Kristin D. Kerrnohan, Alisdair McNeill, Leonie A. Menke, Giuseppe Merla, Paolo Prontera, Cheryl Rockman-Greenberg, Charles Schwartz, Steven A. Skinner, Roger E. Stevenson, Antonio Vitobello, Marco Tartaglia, Marielle Alders, Matthew L. Tedder, Bekim Sadikovic, Levy, Michael A, Mcconkey, Haley, Kerkhof, Jennifer, Barat-Houari, Mouna, Bargiacchi, Sara, Biamino, Elisa, Bralo, María Palomare, Cappuccio, Gerarda, Ciolfi, Andrea, Clarke, Angu, Dupont, Barbara R, Elting, Mariet W, Faivre, Laurence, Fee, Timothy, Fletcher, Robin S, Cherik, Florian, Foroutan, Aidin, Friez, Michael J, Gervasini, Cristina, Haghshenas, Sadegheh, Hilton, Benjamin A, Jenkins, Zandra, Kaur, Simranpreet, Lewis, Suzanne, Louie, Raymond J, Maitz, Silvia, Milani, Donatella, Morgan, Angela T, Oegema, Renske, Østergaard, Elsebet, Pallares, Nathalie Ruiz, Piccione, Maria, Pizzi, Simone, Plomp, Astrid S, Poulton, Cathryn, Reilly, Jack, Relator, Raissa, Rius, Rocio, Robertson, Stephen, Rooney, Kathleen, Rousseau, Justine, Santen, Gijs W E, Santos-Simarro, Fernando, Schijns, Josephine, Squeo, Gabriella Maria, St John, Miya, Thauvin-Robinet, Christel, Traficante, Giovanna, van der Sluijs, Pleuntje J, Vergano, Samantha A, Vos, Niel, Walden, Kellie K, Azmanov, Dimitar, Balci, Tugce, Banka, Siddharth, Gecz, Jozef, Henneman, Peter, Lee, Jennifer A, Mannens, Marcel M A M, Roscioli, Tony, Siu, Victoria, Amor, David J, Baynam, Gareth, Bend, Eric G, Boycott, Kym, Brunetti-Pierri, Nicola, Campeau, Philippe M, Christodoulou, John, Dyment, David, Esber, Natacha, Fahrner, Jill A, Fleming, Mark D, Genevieve, David, Kerrnohan, Kristin D, Mcneill, Alisdair, Menke, Leonie A, Merla, Giuseppe, Prontera, Paolo, Rockman-Greenberg, Cheryl, Schwartz, Charle, Skinner, Steven A, Stevenson, Roger E, Vitobello, Antonio, Tartaglia, Marco, Alders, Marielle, Tedder, Matthew L, Sadikovic, Bekim, Human Genetics, General Paediatrics, Graduate School, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam Reproduction & Development (AR&D), ACS - Pulmonary hypertension & thrombosis, Amsterdam Neuroscience - Cellular & Molecular Mechanisms, and Amsterdam Neuroscience - Complex Trait Genetics
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Clinical diagnostic ,INTELLECTUAL DISABILITY ,COMPLEX ,DNA methylation ,MUTATIONS ,SIGNATURE ,Neurodevelopmental disorders ,Epigenetic ,QH426-470 ,VARIANTS ,Article ,DOMAIN ,Clinical diagnostics ,Genetics ,Molecular Medicine ,Epigenetics ,Episignatures ,COFFIN-SIRIS ,Episignature ,Genetics (clinical) - Abstract
Summary: Overlapping clinical phenotypes and an expanding breadth and complexity of genomic associations are a growing challenge in the diagnosis and clinical management of Mendelian disorders. The functional consequences and clinical impacts of genomic variation may involve unique, disorder-specific, genomic DNA methylation episignatures. In this study, we describe 19 novel episignature disorders and compare the findings alongside 38 previously established episignatures for a total of 57 episignatures associated with 65 genetic syndromes. We demonstrate increasing resolution and specificity ranging from protein complex, gene, sub-gene, protein domain, and even single nucleotide-level Mendelian episignatures. We show the power of multiclass modeling to develop highly accurate and disease-specific diagnostic classifiers. This study significantly expands the number and spectrum of disorders with detectable DNA methylation episignatures, improves the clinical diagnostic capabilities through the resolution of unsolved cases and the reclassification of variants of unknown clinical significance, and provides further insight into the molecular etiology of Mendelian conditions.
- Published
- 2022
29. The ARID1B spectrum in 143 patients
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Catherine Vincent-Delorme, Claudia A. L. Ruivenkamp, Marjan De Rademaeker, Francisco Martínez, Tracy Dudding-Byth, Marianne McGuire, Bert B.A. de Vries, Mitsuhiro Kato, Levinus A. Bok, Hülya Kayserili, Jeff M. Milunsky, Suzanne C E H Sallevelt, Alwin F. J. Brouwer, Jill Clayton-Smith, Emilia K. Bijlsma, Miranda Splitt, Patricia G. Wheeler, Philippe M. Campeau, Fatma Mujgan Sonmez, Kylin Lammers, Stefanie Beck-Wödl, Caroline Rooryck, Louise C. Wilson, Evan E. Eichler, Sarina G. Kant, Johanna C. Herkert, Karin R. Heitink, Eyyup Uctepe, Pleuntje J. van der Sluijs, Miho Adachi-Fukuda, Lone W. Laulund, Sandra Jansen, Nicolette S. den Hollander, Damien Lederer, Tomoki Kosho, Constance T. R. M. Stumpel, Saskia M. Maas, Esra Kılıç, Erica H. Gerkes, Duco Steenbeek, Melissa Lees, Kay Metcalfe, Karin Dahan, Ineke van der Burgt, Isabelle Maystadt, Christian Netzer, Ute Grasshoff, Carmen Orellana, Mahmut Şamil Sağıroğlu, Gijs W. E. Santen, Pelin Ozlem Simsek-Kiper, Mónica Roselló, Gabriela Soares, Alexander P.A. Stegmann, Stephen P. Robertson, Adila Al-Kindy, Maian Roifman, Saori Tanabe, Vera Riehmer, Brain H Y Chung, Arie van Haeringen, G. Eda Utine, Yasemin Alanay, Rogier Kersseboom, John B. Moeschler, Barbara Oehl-Jaschkowitz, Katherine Berry, Denise Horn, Alice Gardham, Shane McKee, Anwar Baban, Amparo Sanchis Calvo, Golder N. Wilson, Krystyna H. Chrzanowska, G. M. S. Mancini, Ellen R. Elias, Małgorzata Krajewska-Walasek, Rolph Pfundt, Sarju G. Mehta, Fabienne G. Ropers, Seiji Mizuno, David Hunt, Caroline Pottinger, Dagmar Wieczorek, Yoyo W. Y. Chu, Laurent Pasquier, Bernd Wollnik, Nobuhiko Okamoto, Sunita Venkateswaran, Vanesa López-González, Natalie Canham, Blanca Gener, Anne Destree, Christina Fagerberg, Rachel K. Earl, Sharon N M Olminkhof, Nursel Elcioglu, Charlotte W. Ockeloen, Carlo Marcelis, Samantha A. Vergano, Hermine E. Veenstra-Knol, Anneke T. Vulto-van Silfhout, Allan Bayat, Catheline Vilain, Lucia Solaeche, MUMC+: DA KG Polikliniek (9), RS: GROW - R4 - Reproductive and Perinatal Medicine, Genetica & Celbiologie, MUMC+: DA KG Lab Centraal Lab (9), MUMC+: DA Pat Cytologie (9), Klinische Genetica, van der Sluijs, Pleuntje J., Jansen, Sandra, Vergano, Samantha A., Adachi-Fukuda, Miho, Alanay, Yasemin, AlKindy, Adila, Baban, Anwar, Bayat, Allan, Beck-Woedl, Stefanie, Berry, Katherine, Bijlsma, Emilia K., Bok, Levinus A., Brouwer, Alwin F. J., van der Burgt, Ineke, Campeau, Philippe M., Canham, Natalie, Chrzanowska, Krystyna, Chu, Yoyo W. Y., Chung, Brain H. Y., Dahan, Karin, De Rademaeker, Marjan, Destree, Anne, Dudding-Byth, Tracy, Earl, Rachel, Elcioglu, Nursel, Elias, Ellen R., Fagerberg, Christina, Gardham, Alice, Gener, Blanca, Gerkes, Erica H., Grasshoff, Ute, van Haeringen, Arie, Heitink, Karin R., Herkert, Johanna C., den Hollander, Nicolette S., Horn, Denise, Hunt, David, Kant, Sarina G., Kato, Mitsuhiro, Kayserili, Hulya, Kersseboom, Rogier, Kilic, Esra, Krajewska-Walasek, Malgorzata, Lammers, Kylin, Laulund, Lone W., Lederer, Damien, Lees, Melissa, Lopez-Gonzalez, Vanesa, Maas, Saskia, Mancini, Grazia M. S., Marcelis, Carlo, Martinez, Francisco, Maystadt, Isabelle, McGuire, Marianne, McKee, Shane, Mehta, Sarju, Metcalfe, Kay, Milunsky, Jeff, Mizuno, Seiji, Moeschler, John B., Netzer, Christian, Ockeloen, Charlotte W., Oehl-Jaschkowitz, Barbara, Okamoto, Nobuhiko, Olminkhof, Sharon N. M., Orellana, Carmen, Pasquier, Laurent, Pottinger, Caroline, Riehmer, Vera, Robertson, Stephen P., Roifman, Maian, Rooryck, Caroline, Ropers, Fabienne G., Rosello, Monica, Ruivenkamp, Claudia A. L., Sagiroglu, Mahmut S., Sallevelt, Suzanne C. E. H., Sanchis Calvo, Amparo, Simsek-Kiper, Pelin O., Soares, Gabriela, Solaeche, Lucia, Sonmez, Fatma Mujgan, Splitt, Miranda, Steenbeek, Duco, Stegmann, Alexander P. A., Stumpel, Constance T. R. M., Tanabe, Saori, Uctepe, Eyyup, Utine, G. Eda, Veenstra-Knol, Hermine E., Venkateswaran, Sunita, Vilain, Catheline, Vincent-Delorme, Catherine, Vulto-van Silfhout, Anneke T., Wheeler, Patricia, Wilson, Golder N., Wilson, Louise C., Wollnik, Bernd, Kosho, Tomoki, Wieczorek, Dagmar, Eichler, Evan, Pfundt, Rolph, de Vries, Bert B. A., Clayton-Smith, Jill, Santen, Gijs W. E., Erasmus MC other, Clinical Genetics, Human Genetics, and Acibadem University Dspace
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Male ,0301 basic medicine ,Hypertrichosis ,Pediatrics ,cuello ,bias ,Coffin–Siris syndrome ,Chromosomal Proteins, Non-Histone ,humanos ,adolescente ,Penetrance ,PHENOTYPE ,0302 clinical medicine ,Genotype ,Intellectual disability ,Exome ,Coffin-Siris syndrome ,Child ,mediana edad ,Genetics (clinical) ,Exome sequencing ,factores de transcripción ,adulto ,Middle Aged ,estudios de asociación genética ,3. Good health ,DNA-Binding Proteins ,intellectual disability ,Child, Preschool ,discapacidad intelectual ,penetrancia ,Female ,Hand Deformities, Congenital ,Rare cancers Radboud Institute for Health Sciences [Radboudumc 9] ,Adult ,medicine.medical_specialty ,Adolescent ,Micrognathism ,Article ,CHROMATIN-REMODELING COMPLEX ,03 medical and health sciences ,All institutes and research themes of the Radboud University Medical Center ,cara ,micrognatismo ,Human Phenotype Ontology ,medicine ,Humans ,Abnormalities, Multiple ,mutación ,Long eyelashes ,Genetic Association Studies ,lactante ,Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7] ,business.industry ,MUTATIONS ,proteínas de unión al ADN ,Infant, Newborn ,Genetic Variation ,Infant ,ARID1B ,Hand Deformities ,Phalanx ,medicine.disease ,variación genética ,deformidades de la mano ,exoma ,030104 developmental biology ,Face ,Mutation ,business ,Neck ,030217 neurology & neurosurgery ,Transcription Factors - Abstract
Purpose: Pathogenic variants in ARID1B are one of the most frequent causes of intellectual disability (ID) as determined by large-scale exome sequencing studies. Most studies published thus far describe clinically diagnosed Coffin-Siris patients (ARID1BCSS) and it is unclear whether these data are representative for patients identified through sequencing of unbiased ID cohorts (ARID1B-ID). We therefore sought to determine genotypic and phenotypic differences between ARID1B-ID and ARID1B-CSS. In parallel, we investigated the effect of different methods of phenotype reporting. Methods: Clinicians entered clinical data in an extensive webbased survey. Results: 79 ARID1B-CSS and 64 ARID1B-ID patients were included. CSS-associated dysmorphic features, such as thick eyebrows, long eyelashes, thick alae nasi, long and/or broad philtrum, small nails and small or absent fifth distal phalanx and hypertrichosis, were observed significantly more often (p < 0.001) in ARID1B-CSS patients. No other significant differences were identified. Conclusion: There are only minor differences between ARID1BID and ARID1B-CSS patients. ARID1B-related disorders seem to consist of a spectrum, and patients should be managed similarly. We demonstrated that data collection methods without an explicit option to report the absence of a feature (such as most Human Phenotype Ontology-based methods) tended to underestimate gene-related features., We are grateful for the assistance of Pepijn Cox in setting up the website www.arid1bgene.com. This study has made use of data generated by the Human Disease Genes website series, www.humandiseasegenes.com. This work was financially supported by grants from the Netherlands Organisation for Health Research and Development (917-86-319 to B.B.A.d.V., 912-12-109 to B.B.A.d.V.)
- Published
- 2019
30. Microduplications of ARID1A and ARID1B cause a novel clinical and epigenetic distinct BAFopathy.
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van der Sluijs PJ, Moutton S, Dingemans AJM, Weis D, Levy MA, Boycott KM, Arberas C, Baldassarri M, Beneteau C, Brusco A, Coutton C, Dabir T, Dentici ML, Devriendt K, Faivre L, van Haelst MM, Jizi K, Kempers MJ, Kerkhof J, Kharbanda M, Lachlan K, Marle N, McConkey H, Mencarelli MA, Mowat D, Niceta M, Nicolas C, Novelli A, Orlando V, Pichon O, Rankin J, Relator R, Ropers FG, Rosenfeld JA, Sachdev R, Sandaradura SA, Shukarova-Angelovska E, Steenbeek D, Tartaglia M, Tedder MA, Trajkova S, Winer N, Woods J, de Vries BBA, Sadikovic B, Alders M, and Santen GWE
- Abstract
Background: ARID1A/ARID1B haploinsufficiency leads to Coffin-Siris syndrome, duplications of ARID1A lead to a distinct clinical syndrome, whilst ARID1B duplications have not yet been linked to a phenotype., Methods: We collected patients with duplications encompassing ARID1A and ARID1B duplications., Results: 16 ARID1A and 13 ARID1B duplication cases were included with duplication sizes ranging from 0.1-1.2 Mb(1-44 genes) for ARID1A and 0.9-10.3 Mb(2-101 genes) for ARID1B. Both groups shared features, with ARID1A patients having more severe intellectual disability, growth delay and congenital anomalies. DNA methylation analysis showed that ARID1A patients had a specific methylation pattern in blood, which differed from controls and from patients with ARID1A or ARID1B loss-of-function variants. ARID1B patients appeared to have a distinct methylation pattern, similar to ARID1A duplication patients, but further research is needed to validate these results. Five cases with duplications including ARID1A or ARID1B initially annotated as duplications of uncertain significance were evaluated using PhenoScore and DNA methylation re-analysis, resulting in the reclassification of two ARID1A and two ARID1B duplications as pathogenic., Conclusion: Our findings reveal that ARID1B duplications manifest a clinical phenotype and ARID1A duplications have a distinct episignature that overlaps with that of ARID1B duplications, providing further evidence for a distinct and emerging BAFopathy caused by whole gene duplication rather than haploinsufficiency., (Copyright © 2024. Published by Elsevier Inc.)
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- 2024
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- View/download PDF
31. Novel diagnostic DNA methylation episignatures expand and refine the epigenetic landscapes of Mendelian disorders.
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Levy MA, McConkey H, Kerkhof J, Barat-Houari M, Bargiacchi S, Biamino E, Bralo MP, Cappuccio G, Ciolfi A, Clarke A, DuPont BR, Elting MW, Faivre L, Fee T, Fletcher RS, Cherik F, Foroutan A, Friez MJ, Gervasini C, Haghshenas S, Hilton BA, Jenkins Z, Kaur S, Lewis S, Louie RJ, Maitz S, Milani D, Morgan AT, Oegema R, Østergaard E, Pallares NR, Piccione M, Pizzi S, Plomp AS, Poulton C, Reilly J, Relator R, Rius R, Robertson S, Rooney K, Rousseau J, Santen GWE, Santos-Simarro F, Schijns J, Squeo GM, St John M, Thauvin-Robinet C, Traficante G, van der Sluijs PJ, Vergano SA, Vos N, Walden KK, Azmanov D, Balci T, Banka S, Gecz J, Henneman P, Lee JA, Mannens MMAM, Roscioli T, Siu V, Amor DJ, Baynam G, Bend EG, Boycott K, Brunetti-Pierri N, Campeau PM, Christodoulou J, Dyment D, Esber N, Fahrner JA, Fleming MD, Genevieve D, Kerrnohan KD, McNeill A, Menke LA, Merla G, Prontera P, Rockman-Greenberg C, Schwartz C, Skinner SA, Stevenson RE, Vitobello A, Tartaglia M, Alders M, Tedder ML, and Sadikovic B
- Abstract
Overlapping clinical phenotypes and an expanding breadth and complexity of genomic associations are a growing challenge in the diagnosis and clinical management of Mendelian disorders. The functional consequences and clinical impacts of genomic variation may involve unique, disorder-specific, genomic DNA methylation episignatures. In this study, we describe 19 novel episignature disorders and compare the findings alongside 38 previously established episignatures for a total of 57 episignatures associated with 65 genetic syndromes. We demonstrate increasing resolution and specificity ranging from protein complex, gene, sub-gene, protein domain, and even single nucleotide-level Mendelian episignatures. We show the power of multiclass modeling to develop highly accurate and disease-specific diagnostic classifiers. This study significantly expands the number and spectrum of disorders with detectable DNA methylation episignatures, improves the clinical diagnostic capabilities through the resolution of unsolved cases and the reclassification of variants of unknown clinical significance, and provides further insight into the molecular etiology of Mendelian conditions., Competing Interests: The authors declare no competing interests., (© 2021 The Author(s).)
- Published
- 2021
- Full Text
- View/download PDF
32. ARID1B -Related Disorder
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Vergano SA, van der Sluijs PJ, Santen G, Adam MP, Ardinger HH, Pagon RA, Wallace SE, Bean LJH, Gripp KW, Mirzaa GM, and Amemiya A
- Abstract
Clinical Characteristics: ARID1B -related disorder ( ARID1B -RD) constitutes a clinical continuum, from classic Coffin-Siris syndrome to intellectual disability with or without nonspecific dysmorphic features. Coffin-Siris syndrome is classically characterized by aplasia or hypoplasia of the distal phalanx or nail of the fifth and additional digits, developmental or cognitive delay of varying degree, distinctive facial features, hypotonia, hypertrichosis, and sparse scalp hair. Frequencies of other features, such as developmental delay (with speech often more affected than motor development), is consistent across the clinical spectrum, and may include malformations of the cardiac, gastrointestinal, genitourinary, and/or central nervous systems. Other findings seen in individuals with ARID1B -RD include feeding difficulties, slow growth, ophthalmologic abnormalities, hearing impairment, seizures, attention-deficit/hyperactivity disorder, and autistic features., Diagnosis/testing: The diagnosis of ARID1B- RD is established by identification of a heterozygous pathogenic variant in ARID1B by molecular genetic testing., Management: Treatment of manifestations: Standard treatment for strabismus, refractive error, hearing loss, congenital heart defects, obstructive sleep apnea, constipation, gastroesophageal reflux, cryptorchidism, scoliosis, and seizure disorders. For significant feeding issues, a nasogastric and/or gastrostomy tube may be required. Developmental therapies, including speech/language and feeding therapy, is recommended for those with developmental delay. Surveillance: At least annual assessment of developmental progress and educational needs; annual ophthalmology evaluation and assessment for scoliosis (until growth is complete). Audiology evaluation, behavior assessment, and hormonal evaluation/bone age as needed based on symptoms. Those with seizures should be monitored as clinically indicated., Genetic Counseling: ARID1B -related disorder is inherited in an autosomal dominant fashion. With the exception of two families in which a parent and child had features consistent with ARID1B -related disorder, all individuals diagnosed to date have the disorder as the result of a de novo pathogenic variant. Once the ARID1B pathogenic variant has been identified in an affected family member, prenatal and preimplantation genetic testing are possible., (Copyright © 1993-2022, University of Washington, Seattle. GeneReviews is a registered trademark of the University of Washington, Seattle. All rights reserved.)
- Published
- 1993
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