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1. The detection of a strong episignature for Chung–Jansen syndrome, partially overlapping with Börjeson–Forssman–Lehmann and White–Kernohan syndromes

Author

Vos, Niels, Haghshenas, Sadegheh, van der Laan, Liselot, Russel, Perle K. M., Rooney, Kathleen, Levy, Michael A., Relator, Raissa, Kerkhof, Jennifer, McConkey, Haley, Maas, Saskia M., Vissers, Lisenka E. L. M., de Vries, Bert B. A., Pfundt, Rolph, Elting, Mariet W., van Hagen, Johanna M., Verbeek, Nienke E., Jongmans, Marjolijn C. J., Lakeman, Phillis, Rumping, Lynne, Bosch, Danielle G. M., Vitobello, Antonio, Thauvin-Robinet, Christel, Faivre, Laurence, Nambot, Sophie, Garde, Aurore, Willems, Marjolaine, Genevieve, David, Nicolas, Gaël, Busa, Tiffany, Toutain, Annick, Gérard, Marion, Bizaoui, Varoona, Isidor, Bertrand, Merla, Giuseppe, Accadia, Maria, Schwartz, Charles E., Ounap, Katrin, Hoffer, Mariëtte J. V., Nezarati, Marjan M., van den Boogaard, Marie-José H., Tedder, Matthew L., Rogers, Curtis, Brusco, Alfredo, Ferrero, Giovanni B., Spodenkiewicz, Marta, Sidlow, Richard, Mussa, Alessandro, Trajkova, Slavica, McCann, Emma, Mroczkowski, Henry J., Jansen, Sandra, Donker-Kaat, Laura, Duijkers, Floor A. M., Stuurman, Kyra E., Mannens, Marcel M. A. M., Alders, Mariëlle, Henneman, Peter, White, Susan M., Sadikovic, Bekim, and van Haelst, Mieke M.

Published
2024
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2. Diagnostic utility of DNA methylation analysis in genetically unsolved pediatric epilepsies and CHD2 episignature refinement

Author

LaFlamme, Christy W., Rastin, Cassandra, Sengupta, Soham, Pennington, Helen E., Russ-Hall, Sophie J., Schneider, Amy L., Bonkowski, Emily S., Almanza Fuerte, Edith P., Allan, Talia J., Zalusky, Miranda Perez-Galey, Goffena, Joy, Gibson, Sophia B., Nyaga, Denis M., Lieffering, Nico, Hebbar, Malavika, Walker, Emily V., Darnell, Daniel, Olsen, Scott R., Kolekar, Pandurang, Djekidel, Mohamed Nadhir, Rosikiewicz, Wojciech, McConkey, Haley, Kerkhof, Jennifer, Levy, Michael A., Relator, Raissa, Lev, Dorit, Lerman-Sagie, Tally, Park, Kristen L., Alders, Marielle, Cappuccio, Gerarda, Chatron, Nicolas, Demain, Leigh, Genevieve, David, Lesca, Gaetan, Roscioli, Tony, Sanlaville, Damien, Tedder, Matthew L., Gupta, Sachin, Jones, Elizabeth A., Weisz-Hubshman, Monika, Ketkar, Shamika, Dai, Hongzheng, Worley, Kim C., Rosenfeld, Jill A., Chao, Hsiao-Tuan, Neale, Geoffrey, Carvill, Gemma L., Wang, Zhaoming, Berkovic, Samuel F., Sadleir, Lynette G., Miller, Danny E., Scheffer, Ingrid E., Sadikovic, Bekim, and Mefford, Heather C.

Published
2024
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3. Identification of a DNA methylation episignature for recurrent constellations of embryonic malformations

Author

Haghshenas, Sadegheh, Karimi, Karim, Stevenson, Roger E., Levy, Michael A., Relator, Raissa, Kerkhof, Jennifer, Rzasa, Jessica, McConkey, Haley, Lauzon-Young, Carolyn, Balci, Tugce B., White-Brown, Alexandre M., Carter, Melissa T., Richer, Julie, Armour, Christine M., Sawyer, Sarah L., Bhola, Priya T., Tedder, Matthew L., Skinner, Cindy D., van Rooij, Iris A.L.M., van de Putte, Romy, de Blaauw, Ivo, Koeck, Rebekka M., Hoischen, Alexander, Brunner, Han, Esteki, Masoud Zamani, Pelet, Anna, Lyonnet, Stanislas, Amiel, Jeanne, Boycott, Kym M., and Sadikovic, Bekim

Published
2024
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4. Comprehensive EHMT1 variants analysis broadens genotype-phenotype associations and molecular mechanisms in Kleefstra syndrome

Author

Rots, Dmitrijs, Bouman, Arianne, Yamada, Ayumi, Levy, Michael, Dingemans, Alexander J.M., de Vries, Bert B.A., Ruiterkamp-Versteeg, Martina, de Leeuw, Nicole, Ockeloen, Charlotte W., Pfundt, Rolph, de Boer, Elke, Kummeling, Joost, van Bon, Bregje, van Bokhoven, Hans, Kasri, Nael Nadif, Venselaar, Hanka, Alders, Marielle, Kerkhof, Jennifer, McConkey, Haley, Kuechler, Alma, Elffers, Bart, van Beeck Calkoen, Rixje, Hofman, Susanna, Smith, Audrey, Valenzuela, Maria Irene, Srivastava, Siddharth, Frazier, Zoe, Maystadt, Isabelle, Piscopo, Carmelo, Merla, Giuseppe, Balasubramanian, Meena, Santen, Gijs W.E., Metcalfe, Kay, Park, Soo-Mi, Pasquier, Laurent, Banka, Siddharth, Donnai, Dian, Weisberg, Daniel, Strobl-Wildemann, Gertrud, Wagemans, Annemieke, Vreeburg, Maaike, Baralle, Diana, Foulds, Nicola, Scurr, Ingrid, Brunetti-Pierri, Nicola, van Hagen, Johanna M., Bijlsma, Emilia K., Hakonen, Anna H., Courage, Carolina, Genevieve, David, Pinson, Lucile, Forzano, Francesca, Deshpande, Charu, Kluskens, Maria L., Welling, Lindsey, Plomp, Astrid S., Vanhoutte, Els K., Kalsner, Louisa, Hol, Janna A., Putoux, Audrey, Lazier, Johanna, Vasudevan, Pradeep, Ames, Elizabeth, O'Shea, Jessica, Lederer, Damien, Fleischer, Julie, O'Connor, Mary, Pauly, Melissa, Vasileiou, Georgia, Reis, André, Kiraly-Borri, Catherine, Bouman, Arjan, Barnett, Chris, Nezarati, Marjan, Borch, Lauren, Beunders, Gea, Özcan, Kübra, Miot, Stéphanie, Volker-Touw, Catharina M.L., van Gassen, Koen L.I., Cappuccio, Gerarda, Janssens, Katrien, Mor, Nofar, Shomer, Inna, Dominissini, Dan, Tedder, Matthew L., Muir, Alison M., Sadikovic, Bekim, Brunner, Han G., Vissers, Lisenka E.L.M., Shinkai, Yoichi, and Kleefstra, Tjitske

Published
2024
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6. Diagnostic utility and reporting recommendations for clinical DNA methylation episignature testing in genetically undiagnosed rare diseases

Author

Kerkhof, Jennifer, Rastin, Cassandra, Levy, Michael A., Relator, Raissa, McConkey, Haley, Demain, Leigh, Dominguez-Garrido, Elena, Kaat, Laura Donker, Houge, Sofia Douzgou, DuPont, Barbara R., Fee, Timothy, Fletcher, Robin S., Gokhale, David, Haukanes, Bjørn Ivar, Henneman, Peter, Hilton, Sarah, Hilton, Benjamin A., Jenkinson, Sarah, Lee, Jennifer A., Louie, Raymond J., Motazacker, M. Mahdi, Rzasa, Jessica, Stevenson, Roger E., Plomp, Astrid, van der Laan, Liselot, van der Smagt, Jasper, Walden, Kellie K., Banka, Siddharth, Mannens, Marcel, Skinner, Steven A., Friez, Michael J., Campbell, Christopher, Tedder, Matthew L., Alders, Marielle, and Sadikovic, Bekim

Published
2024
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7. Identification of DNA methylation episignature for the intellectual developmental disorder, autosomal dominant 21 syndrome, caused by variants in the CTCF gene

Author

Karimi, Karim, Mol, Merel O., Haghshenas, Sadegheh, Relator, Raissa, Levy, Michael A., Kerkhof, Jennifer, McConkey, Haley, Brooks, Alice, Zonneveld-Huijssoon, Evelien, Gerkes, Erica H., Tedder, Matthew L., Vissers, Lisenka, Salzano, Emanuela, Piccione, Maria, Asaftei, Sebastian Dorin, Carli, Diana, Mussa, Alessandro, Shukarova-Angelovska, Elena, Trajkova, Slavica, Brusco, Alfredo, Merla, Giuseppe, Alders, Marielle M., Bouman, Arjan, and Sadikovic, Bekim

Published
2024
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8. Clinical findings and a DNA methylation signature in kindreds with alterations in ZNF711

Author

Wang, Jiyong, Foroutan, Aidin, Richardson, Ellen, Skinner, Steven A., Reilly, Jack, Kerkhof, Jennifer, Curry, Cynthia J., Tarpey, Patrick S., Robertson, Stephen P., Maystadt, Isabelle, Keren, Boris, Dixon, Joanne W., Skinner, Cindy, Stapleton, Rachel, Ruaud, Lyse, Gumus, Evren, Lakeman, Phillis, Alders, Mariëlle, Tedder, Matthew L., Schwartz, Charles E., Friez, Michael J., Sadikovic, Bekim, and Stevenson, Roger E.

Published
2022
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9. The phenotypic spectrum and genotype-phenotype correlations in 106 patients with variants in major autism gene CHD8

Author

Dingemans, Alexander J. M., Truijen, Kim M. G., van de Ven, Sam, Bernier, Raphael, Bongers, Ernie M. H. F., Bouman, Arjan, de Graaff – Herder, Laura, Eichler, Evan E., Gerkes, Erica H., De Geus, Christa M., van Hagen, Johanna M., Jansen, Philip R., Kerkhof, Jennifer, Kievit, Anneke J. A., Kleefstra, Tjitske, Maas, Saskia M., de Man, Stella A., McConkey, Haley, Patterson, Wesley G., Dobson, Amy T., Prijoles, Eloise J., Sadikovic, Bekim, Relator, Raissa, Stevenson, Roger E., Stumpel, Connie T. R. M., Heijligers, Malou, Stuurman, Kyra E., Löhner, Katharina, Zeidler, Shimriet, Lee, Jennifer A., Lindy, Amanda, Zou, Fanggeng, Tedder, Matthew L., Vissers, Lisenka E. L. M., and de Vries, Bert B. A.

Published
2022
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10. Clinical epigenomics: genome-wide DNA methylation analysis for the diagnosis of Mendelian disorders

Author

Sadikovic, Bekim, Levy, Michael A., Kerkhof, Jennifer, Aref-Eshghi, Erfan, Schenkel, Laila, Stuart, Alan, McConkey, Haley, Henneman, Peter, Venema, Andrea, Schwartz, Charles E., Stevenson, Roger E., Skinner, Steven A., DuPont, Barbara R., Fletcher, Robin S., Balci, Tugce B., Siu, Victoria Mok, Granadillo, Jorge L., Masters, Jennefer, Kadour, Mike, Friez, Michael J., van Haelst, Mieke M., Mannens, Marcel M. A. M., Louie, Raymond J., Lee, Jennifer A., Tedder, Matthew L., and Alders, Marielle

Published
2021
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11. Diagnostic utility and reporting recommendations for clinical DNA methylation episignature testing in genetically undiagnosed rare diseases

Author

Genetica, Genetica Klinische Genetica, Circulatory Health, Kerkhof, Jennifer, Rastin, Cassandra, Levy, Michael A., Relator, Raissa, McConkey, Haley, Demain, Leigh, Dominguez-Garrido, Elena, Kaat, Laura Donker, Houge, Sofia Douzgou, DuPont, Barbara R., Fee, Timothy, Fletcher, Robin S., Gokhale, David, Haukanes, Bjørn Ivar, Henneman, Peter, Hilton, Sarah, Hilton, Benjamin A., Jenkinson, Sarah, Lee, Jennifer A., Louie, Raymond J., Motazacker, M. Mahdi, Rzasa, Jessica, Stevenson, Roger E., Plomp, Astrid, van der Laan, Liselot, van der Smagt, Jasper, Walden, Kellie K., Banka, Siddharth, Mannens, Marcel, Skinner, Steven A., Friez, Michael J., Campbell, Christopher, Tedder, Matthew L., Alders, Marielle, Sadikovic, Bekim, Genetica, Genetica Klinische Genetica, Circulatory Health, Kerkhof, Jennifer, Rastin, Cassandra, Levy, Michael A., Relator, Raissa, McConkey, Haley, Demain, Leigh, Dominguez-Garrido, Elena, Kaat, Laura Donker, Houge, Sofia Douzgou, DuPont, Barbara R., Fee, Timothy, Fletcher, Robin S., Gokhale, David, Haukanes, Bjørn Ivar, Henneman, Peter, Hilton, Sarah, Hilton, Benjamin A., Jenkinson, Sarah, Lee, Jennifer A., Louie, Raymond J., Motazacker, M. Mahdi, Rzasa, Jessica, Stevenson, Roger E., Plomp, Astrid, van der Laan, Liselot, van der Smagt, Jasper, Walden, Kellie K., Banka, Siddharth, Mannens, Marcel, Skinner, Steven A., Friez, Michael J., Campbell, Christopher, Tedder, Matthew L., Alders, Marielle, and Sadikovic, Bekim

Published
2024

12. The detection of a strong episignature for Chung-Jansen syndrome, partially overlapping with Börjeson-Forssman-Lehmann and White-Kernohan syndromes

Author

Genetica Klinische Genetica, Cancer, Child Health, Vos, Niels, Haghshenas, Sadegheh, van der Laan, Liselot, Russel, Perle K M, Rooney, Kathleen, Levy, Michael A, Relator, Raissa, Kerkhof, Jennifer, McConkey, Haley, Maas, Saskia M, Vissers, Lisenka E L M, de Vries, Bert B A, Pfundt, Rolph, Elting, Mariet W, van Hagen, Johanna M, Verbeek, Nienke E, Jongmans, Marjolijn C J, Lakeman, Phillis, Rumping, Lynne, Bosch, Danielle G M, Vitobello, Antonio, Thauvin-Robinet, Christel, Faivre, Laurence, Nambot, Sophie, Garde, Aurore, Willems, Marjolaine, Genevieve, David, Nicolas, Gaël, Busa, Tiffany, Toutain, Annick, Gérard, Marion, Bizaoui, Varoona, Isidor, Bertrand, Merla, Giuseppe, Accadia, Maria, Schwartz, Charles E, Ounap, Katrin, Hoffer, Mariëtte J V, Nezarati, Marjan M, van den Boogaard, Marie-José H, Tedder, Matthew L, Rogers, Curtis, Brusco, Alfredo, Ferrero, Giovanni B, Spodenkiewicz, Marta, Sidlow, Richard, Mussa, Alessandro, Trajkova, Slavica, McCann, Emma, Mroczkowski, Henry J, Jansen, Sandra, Donker-Kaat, Laura, Duijkers, Floor A M, Stuurman, Kyra E, Mannens, Marcel M A M, Alders, Mariëlle, Henneman, Peter, White, Susan M, Sadikovic, Bekim, van Haelst, Mieke M, Genetica Klinische Genetica, Cancer, Child Health, Vos, Niels, Haghshenas, Sadegheh, van der Laan, Liselot, Russel, Perle K M, Rooney, Kathleen, Levy, Michael A, Relator, Raissa, Kerkhof, Jennifer, McConkey, Haley, Maas, Saskia M, Vissers, Lisenka E L M, de Vries, Bert B A, Pfundt, Rolph, Elting, Mariet W, van Hagen, Johanna M, Verbeek, Nienke E, Jongmans, Marjolijn C J, Lakeman, Phillis, Rumping, Lynne, Bosch, Danielle G M, Vitobello, Antonio, Thauvin-Robinet, Christel, Faivre, Laurence, Nambot, Sophie, Garde, Aurore, Willems, Marjolaine, Genevieve, David, Nicolas, Gaël, Busa, Tiffany, Toutain, Annick, Gérard, Marion, Bizaoui, Varoona, Isidor, Bertrand, Merla, Giuseppe, Accadia, Maria, Schwartz, Charles E, Ounap, Katrin, Hoffer, Mariëtte J V, Nezarati, Marjan M, van den Boogaard, Marie-José H, Tedder, Matthew L, Rogers, Curtis, Brusco, Alfredo, Ferrero, Giovanni B, Spodenkiewicz, Marta, Sidlow, Richard, Mussa, Alessandro, Trajkova, Slavica, McCann, Emma, Mroczkowski, Henry J, Jansen, Sandra, Donker-Kaat, Laura, Duijkers, Floor A M, Stuurman, Kyra E, Mannens, Marcel M A M, Alders, Mariëlle, Henneman, Peter, White, Susan M, Sadikovic, Bekim, and van Haelst, Mieke M

Published
2024

13. Comprehensive EHMT1 variants analysis broadens genotype-phenotype associations and molecular mechanisms in Kleefstra syndrome

Author

Genetica, Genetica Klinische Genetica, Genetica Sectie Genoomdiagnostiek, Child Health, Rots, Dmitrijs, Bouman, Arianne, Yamada, Ayumi, Levy, Michael, Dingemans, Alexander J.M., de Vries, Bert B.A., Ruiterkamp-Versteeg, Martina, de Leeuw, Nicole, Ockeloen, Charlotte W., Pfundt, Rolph, de Boer, Elke, Kummeling, Joost, van Bon, Bregje, van Bokhoven, Hans, Kasri, Nael Nadif, Venselaar, Hanka, Alders, Marielle, Kerkhof, Jennifer, McConkey, Haley, Kuechler, Alma, Elffers, Bart, van Beeck Calkoen, Rixje, Hofman, Susanna, Smith, Audrey, Valenzuela, Maria Irene, Srivastava, Siddharth, Frazier, Zoe, Maystadt, Isabelle, Piscopo, Carmelo, Merla, Giuseppe, Balasubramanian, Meena, Santen, Gijs W.E., Metcalfe, Kay, Park, Soo Mi, Pasquier, Laurent, Banka, Siddharth, Donnai, Dian, Weisberg, Daniel, Strobl-Wildemann, Gertrud, Wagemans, Annemieke, Vreeburg, Maaike, Baralle, Diana, Foulds, Nicola, Scurr, Ingrid, Brunetti-Pierri, Nicola, van Hagen, Johanna M., Bijlsma, Emilia K., Hakonen, Anna H., Courage, Carolina, Genevieve, David, Pinson, Lucile, Forzano, Francesca, Deshpande, Charu, Kluskens, Maria L., Welling, Lindsey, Plomp, Astrid S., Vanhoutte, Els K., Kalsner, Louisa, Hol, Janna A., Putoux, Audrey, Lazier, Johanna, Vasudevan, Pradeep, Ames, Elizabeth, O'Shea, Jessica, Lederer, Damien, Fleischer, Julie, O'Connor, Mary, Pauly, Melissa, Vasileiou, Georgia, Reis, André, Kiraly-Borri, Catherine, Bouman, Arjan, Barnett, Chris, Nezarati, Marjan, Borch, Lauren, Beunders, Gea, Özcan, Kübra, Miot, Stéphanie, Volker-Touw, Catharina M.L., van Gassen, Koen L.I., Cappuccio, Gerarda, Janssens, Katrien, Mor, Nofar, Shomer, Inna, Dominissini, Dan, Tedder, Matthew L., Muir, Alison M., Sadikovic, Bekim, Brunner, Han G., Vissers, Lisenka E.L.M., Shinkai, Yoichi, Kleefstra, Tjitske, Genetica, Genetica Klinische Genetica, Genetica Sectie Genoomdiagnostiek, Child Health, Rots, Dmitrijs, Bouman, Arianne, Yamada, Ayumi, Levy, Michael, Dingemans, Alexander J.M., de Vries, Bert B.A., Ruiterkamp-Versteeg, Martina, de Leeuw, Nicole, Ockeloen, Charlotte W., Pfundt, Rolph, de Boer, Elke, Kummeling, Joost, van Bon, Bregje, van Bokhoven, Hans, Kasri, Nael Nadif, Venselaar, Hanka, Alders, Marielle, Kerkhof, Jennifer, McConkey, Haley, Kuechler, Alma, Elffers, Bart, van Beeck Calkoen, Rixje, Hofman, Susanna, Smith, Audrey, Valenzuela, Maria Irene, Srivastava, Siddharth, Frazier, Zoe, Maystadt, Isabelle, Piscopo, Carmelo, Merla, Giuseppe, Balasubramanian, Meena, Santen, Gijs W.E., Metcalfe, Kay, Park, Soo Mi, Pasquier, Laurent, Banka, Siddharth, Donnai, Dian, Weisberg, Daniel, Strobl-Wildemann, Gertrud, Wagemans, Annemieke, Vreeburg, Maaike, Baralle, Diana, Foulds, Nicola, Scurr, Ingrid, Brunetti-Pierri, Nicola, van Hagen, Johanna M., Bijlsma, Emilia K., Hakonen, Anna H., Courage, Carolina, Genevieve, David, Pinson, Lucile, Forzano, Francesca, Deshpande, Charu, Kluskens, Maria L., Welling, Lindsey, Plomp, Astrid S., Vanhoutte, Els K., Kalsner, Louisa, Hol, Janna A., Putoux, Audrey, Lazier, Johanna, Vasudevan, Pradeep, Ames, Elizabeth, O'Shea, Jessica, Lederer, Damien, Fleischer, Julie, O'Connor, Mary, Pauly, Melissa, Vasileiou, Georgia, Reis, André, Kiraly-Borri, Catherine, Bouman, Arjan, Barnett, Chris, Nezarati, Marjan, Borch, Lauren, Beunders, Gea, Özcan, Kübra, Miot, Stéphanie, Volker-Touw, Catharina M.L., van Gassen, Koen L.I., Cappuccio, Gerarda, Janssens, Katrien, Mor, Nofar, Shomer, Inna, Dominissini, Dan, Tedder, Matthew L., Muir, Alison M., Sadikovic, Bekim, Brunner, Han G., Vissers, Lisenka E.L.M., Shinkai, Yoichi, and Kleefstra, Tjitske

Published
2024

14. DNA methylation episignatures are sensitive and specific biomarkers for detection of patients with KAT6A/KAT6B variants

Author

Vos, Niels, Reilly, Jack, Elting, Mariet W., Campeau, Philippe M., Coman, David, Stark, Zornitza, Tan, Tiong Yang, Amor, David J., Kaur, Simran, StJohn, Miya, Morgan, Angela T., Kamien, Benjamin A., Patel, Chirag, Tedder, Matthew L., Merla, Giuseppe, Prontera, Paolo, Castori, Marco, Muru, Kai, Collins, Felicity, Christodoulou, John, Smith, Janine, Zeev, Bruria Ben, Murgia, Alessandra, Leonardi, Emanuela, Esber, Natacha, Martinez-Monseny, Antonio, Casas-Alba, Didac, Wallis, Matthew, Mannens, Marcel, Levy, Michael A., Relator, Raissa, Alders, Marielle, Sadikovic, Bekim, Human genetics, and Amsterdam Reproduction & Development (AR&D)

Abstract

Accurate diagnosis for patients living with neurodevelopmental disorders is often met with numerous challenges, related to the ambiguity of findings and lack of specificity in genetic variants leading to pathology. Genome-wide DNA methylation analysis has been used to develop highly sensitive and specific 'episignatures' as biomarkers capable of differentiating and classifying complex neurodevelopmental disorders. In this study we describe distinct episignatures for KAT6A syndrome, caused by pathogenic variants in the lysine acetyltransferase A gene (KAT6A), and for the two neurodevelopmental disorders associated with lysine acetyl transferase B (KAT6B). We demonstrate the ability of our models to differentiate between highly overlapping episignatures, increasing the ability to effectively identify and diagnose these conditions.

Published
2023

15. DNA methylation episignature for Witteveen-Kolk syndrome due to SIN3A haploinsufficiency

Author

Coenen-van der Spek, Jet, primary, Relator, Raissa, additional, Kerkhof, Jennifer, additional, McConkey, Haley, additional, Levy, Michael A., additional, Tedder, Matthew L., additional, Louie, Raymond J., additional, Fletcher, Robin S., additional, Moore, Hannah W., additional, Childers, Anna, additional, Farrelly, Ellyn R., additional, Champaigne, Neena L., additional, Lyons, Michael J., additional, Everman, David B., additional, Rogers, R. Curtis, additional, Skinner, Steven A., additional, Renck, Alicia, additional, Matalon, Dena R., additional, Dills, Shelley K., additional, Monteleone, Berrin, additional, Demirdas, Serwet, additional, Dingemans, Alexander J.M., additional, Donker Kaat, Laura, additional, Kolk, Sharon M., additional, Pfundt, Rolph, additional, Rump, Patrick, additional, Sadikovic, Bekim, additional, Kleefstra, Tjitske, additional, and Butler, Kameryn M., additional

Published
2023
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16. Episignature Mapping of TRIP12 Provides Functional Insight into Clark–Baraitser Syndrome

Author

van der Laan, Liselot, primary, Rooney, Kathleen, additional, Alders, Mariëlle, additional, Relator, Raissa, additional, McConkey, Haley, additional, Kerkhof, Jennifer, additional, Levy, Michael A., additional, Lauffer, Peter, additional, Aerden, Mio, additional, Theunis, Miel, additional, Legius, Eric, additional, Tedder, Matthew L., additional, Vissers, Lisenka E. L. M., additional, Koene, Saskia, additional, Ruivenkamp, Claudia, additional, Hoffer, Mariette J. V., additional, Wieczorek, Dagmar, additional, Bramswig, Nuria C., additional, Herget, Theresia, additional, González, Vanesa López, additional, Santos-Simarro, Fernando, additional, Tørring, Pernille M., additional, Denomme-Pichon, Anne-Sophie, additional, Isidor, Bertrand, additional, Keren, Boris, additional, Julia, Sophie, additional, Schaefer, Elise, additional, Francannet, Christine, additional, Maillard, Pierre-Yves, additional, Misra-Isrie, Mala, additional, Van Esch, Hilde, additional, Mannens, Marcel M. A. M., additional, Sadikovic, Bekim, additional, van Haelst, Mieke M., additional, and Henneman, Peter, additional

Published
2022
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17. Functional correlation of genome‐wide DNA methylation profiles in genetic neurodevelopmental disorders

Author

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

Published
2022
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19. Novel diagnostic DNA methylation episignatures expand and refine the epigenetic landscapes of Mendelian disorders

Author

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

20. Functional correlation of genome-wide DNA methylation profiles in genetic neurodevelopmental disorders

Author

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

21. The phenotypic spectrum and genotype-phenotype correlations in 106 patients with variants in major autism gene CHD8

Author

Dingemans, Alexander J.M., Truijen, Kim M.G., van de Ven, Sam, Bernier, Raphael, Bongers, Ernie M.H.F., Bouman, Arjan, de Graaff – Herder, Laura, Eichler, Evan E., Gerkes, Erica H., De Geus, Christa M., van Hagen, Johanna M., Jansen, Philip R., Kerkhof, Jennifer, Kievit, Anneke J.A., Kleefstra, Tjitske, Maas, Saskia M., de Man, Stella A., McConkey, Haley, Patterson, Wesley G., Dobson, Amy T., Prijoles, Eloise J., Sadikovic, Bekim, Relator, Raissa, Stevenson, Roger E., Stumpel, Connie T.R.M., Heijligers, Malou, Stuurman, Kyra E., Löhner, Katharina, Zeidler, Shimriet, Lee, Jennifer A., Lindy, Amanda, Zou, Fanggeng, Tedder, Matthew L., Vissers, Lisenka E.L.M., de Vries, Bert B.A., Dingemans, Alexander J.M., Truijen, Kim M.G., van de Ven, Sam, Bernier, Raphael, Bongers, Ernie M.H.F., Bouman, Arjan, de Graaff – Herder, Laura, Eichler, Evan E., Gerkes, Erica H., De Geus, Christa M., van Hagen, Johanna M., Jansen, Philip R., Kerkhof, Jennifer, Kievit, Anneke J.A., Kleefstra, Tjitske, Maas, Saskia M., de Man, Stella A., McConkey, Haley, Patterson, Wesley G., Dobson, Amy T., Prijoles, Eloise J., Sadikovic, Bekim, Relator, Raissa, Stevenson, Roger E., Stumpel, Connie T.R.M., Heijligers, Malou, Stuurman, Kyra E., Löhner, Katharina, Zeidler, Shimriet, Lee, Jennifer A., Lindy, Amanda, Zou, Fanggeng, Tedder, Matthew L., Vissers, Lisenka E.L.M., and de Vries, Bert B.A.

Abstract

CHD8, a major autism gene, functions in chromatin remodelling and has various roles involving several biological pathways. Therefore, unsurprisingly, previous studies have shown that intellectual developmental disorder with autism and macrocephaly (IDDAM), the syndrome caused by pathogenic variants in CHD8, consists of a broad range of phenotypic abnormalities. We collected and reviewed 106 individuals with IDDAM, including 36 individuals not previously published, thus enabling thorough genotype–phenotype analyses, involving the CHD8 mutation spectrum, characterization of the CHD8 DNA methylation episignature, and the systematic analysis of phenotypes collected in Human Phenotype Ontology (HPO). We identified 29 unique nonsense, 25 frameshift, 24 missense, and 12 splice site variants. Furthermore, two unique inframe deletions, one larger deletion (exons 26–28), and one translocation were observed. Methylation analysis was performed for 13 patients, 11 of which showed the previously established episignature for IDDAM (85%) associated with CHD8 haploinsufficiency, one analysis was inconclusive, and one showing a possible gain-of-function signature instead of the expected haploinsufficiency signature was observed. Consistent with previous studies, phenotypical abnormalities affected multiple organ systems. Many neurological abnormalities, like intellectual disability (68%) and hypotonia (29%) were observed, as well as a wide variety of behavioural abnormalities (88%). Most frequently observed behavioural problems included autism spectrum disorder (76%), short attention span (32%), abnormal social behaviour (31%), sleep disturbance (29%) and impaired social interactions (28%). Furthermore, abnormalities in the digestive (53%), musculoskeletal (79%) and genitourinary systems (18%) were noted. Although no significant difference in severity was observed between males and females, individuals with a missense variant were less severely affected. Our study provides an exte

Published
2022

22. Functional correlation of genome-wide DNA methylation profiles in genetic neurodevelopmental disorders

Author

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

23. DNA methylation episignature in Gabriele-de Vries syndrome

Author

Cherik, Florian, primary, Reilly, Jack, additional, Kerkhof, Jennifer, additional, Levy, Michael, additional, McConkey, Haley, additional, Barat-Houari, Mouna, additional, Butler, Kameryn M., additional, Coubes, Christine, additional, Lee, Jennifer A., additional, Le Guyader, Gwenael, additional, Louie, Raymond J., additional, Patterson, Wesley G., additional, Tedder, Matthew L., additional, Bak, Mads, additional, Hammer, Trine Bjørg, additional, Craigen, William, additional, Démurger, Florence, additional, Dubourg, Christèle, additional, Fradin, Mélanie, additional, Franciskovich, Rachel, additional, Frengen, Eirik, additional, Friedman, Jennifer, additional, Palares, Nathalie Ruiz, additional, Iascone, Maria, additional, Misceo, Doriana, additional, Monin, Pauline, additional, Odent, Sylvie, additional, Philippe, Christophe, additional, Rouxel, Flavien, additional, Saletti, Veronica, additional, Strømme, Petter, additional, Thulin, Perla Cassayre, additional, Sadikovic, Bekim, additional, and Genevieve, David, additional

Published
2022
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24. Near complete deletion ofKMT2Din a college student

Author

Gooch, Catherine, primary, Souder, Jaclyn Paige, additional, Tedder, Matthew L., additional, Kerkhof, Jennifer, additional, Lee, Jennifer A., additional, Louie, Raymond J., additional, Sadikovic, Bekim, additional, Fletcher, Robin S., additional, and Robin, Nathaniel H., additional

Published
2022
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25. Novel diagnostic DNA methylation episignatures expand and refine the epigenetic landscapes of Mendelian disorders

Author

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
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26. Correction: Clinical epigenomics: genome-wide DNA methylation analysis for the diagnosis of Mendelian disorders (Genetics in Medicine, (2021), 23, 6, (1065-1074), 10.1038/s41436-020-01096-4)

Author

Sadikovic, Bekim, Levy, Michael A., Kerkhof, Jennifer, Aref-Eshghi, Erfan, Schenkel, Laila, Stuart, Alan, McConkey, Haley, Henneman, Peter, Venema, Andrea, Schwartz, Charles E., Stevenson, Roger E., Skinner, Steven A., DuPont, Barbara R., Fletcher, Robin S., Balci, Tugce B., Siu, Victoria Mok, Granadillo, Jorge L., Masters, Jennefer, Kadour, Mike, Friez, Michael J., van Haelst, Mieke M., Mannens, Marcel M. A. M., Louie, Raymond J., Lee, Jennifer A., Tedder, Matthew L., Alders, Marielle, Human genetics, Amsterdam Neuroscience - Complex Trait Genetics, Amsterdam Reproduction & Development (AR&D), Human Genetics, Amsterdam Gastroenterology Endocrinology Metabolism, and ACS - Pulmonary hypertension & thrombosis

Abstract

A Correction to this paper has been published: https://doi.org/10.1038/s41436-021-01130-z.

Published
2021

27. Identification of a DNA Methylation Episignature in the 22q11.2 Deletion Syndrome

Author

Rooney, Kathleen, primary, Levy, Michael A., additional, Haghshenas, Sadegheh, additional, Kerkhof, Jennifer, additional, Rogaia, Daniela, additional, Tedesco, Maria Giovanna, additional, Imperatore, Valentina, additional, Mencarelli, Amedea, additional, Squeo, Gabriella Maria, additional, Di Venere, Eleonora, additional, Di Cara, Giuseppe, additional, Verrotti, Alberto, additional, Merla, Giuseppe, additional, Tedder, Matthew L., additional, DuPont, Barbara R., additional, Sadikovic, Bekim, additional, and Prontera, Paolo, additional

Published
2021
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29. Near complete deletion of KMT2D in a college student.

Author

Gooch, Catherine, Souder, Jaclyn Paige, Tedder, Matthew L., Kerkhof, Jennifer, Lee, Jennifer A., Louie, Raymond J., Sadikovic, Bekim, Fletcher, Robin S., and Robin, Nathaniel H.

Abstract

Pathogenic variants in KMT2D are typically associated with Kabuki syndrome (KS), a rare multisystem disorder. KS is characterized by facial dysmorphisms, intellectual disability, skeletal and dermatoglyphic differences, and poor growth. Seventy percent of individuals with clinically diagnosed KS have a confirmed pathogenic variant in KMT2D or less commonly KDM6A. The majority of mutations found in KMT2D are de novo nonsense or frameshift, with deletions and duplications rarely reported in the literature. Here, we present the case of near complete deletion of KMT2D in a college student with normal intelligence discovered via exome sequencing and EpiSign methylation testing. This case provides evidence that large deletions in KMT2D are compatible with normal intelligence and presents EpiSign as a method for discovering molecular causes of KS not identified by traditional molecular testing. [ABSTRACT FROM AUTHOR]

Published
2022
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30. Discovery of a novel CHD7 CHARGE syndrome variant by integrated omics analyses.

Author

Granadillo, Jorge L., Wegner, Daniel J., Paul, Alexander J., Willing, Marcia, Sisco, Kathleen, Tedder, Matthew L., Sadikovic, Bekim, Wambach, Jennifer A., Baldridge, Dustin, and Cole, Francis Sessions

Abstract

Chromodomain helicase DNA‐binding protein 7 (CHD7) pathogenic variants are identified in more than 90% of infants and children with CHARGE (Coloboma of the iris, retina, and/or optic disk; congenital Heart defects, choanal Atresia, Retardation of growth and development, Genital hypoplasia, and characteristic outer and inner Ear anomalies and deafness) syndrome. Approximately, 10% of cases have no known genetic cause identified. We report a male child with clinical features of CHARGE syndrome and nondiagnostic genetic testing that included chromosomal microarray, CHD7 sequencing and deletion/duplication analysis, SEMA3E sequencing, and trio exome and whole‐genome sequencing (WGS). We used a comprehensive clinical assessment, genome‐wide methylation analysis (GMA), reanalysis of WGS data, and CHD7 RNA studies to discover a novel variant that causes CHD7 haploinsufficiency. The 7‐year‐old Hispanic male proband has typical phenotypic features of CHARGE syndrome. GMA revealed a CHD7‐associated epigenetic signature. Reanalysis of the WGS data with focused bioinformatic analysis of CHD7 detected a novel, de novo 15 base pair deletion in Intron 4 of CHD7 (c.2239‐20_2239‐6delGTCTTGGGTTTTTGT [NM_017780.3]). Using proband RNA, we confirmed that this novel deletion causes CHD7 haploinsufficiency by disrupting the canonical 3′ splice site and introducing a premature stop codon. Integrated genomic, epigenomic, and transcriptome analyses discovered a novel CHD7 variant that causes CHARGE syndrome. [ABSTRACT FROM AUTHOR]

Published
2021
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31. Correction: Clinical findings and a DNA methylation signature in kindreds with alterations in ZNF711

Author

Wang, Jiyong, Foroutan, Aidin, Richardson, Ellen, Skinner, Steven A., Reilly, Jack, Kerkhof, Jennifer, Curry, Cynthia J., Tarpey, Patrick S., Robertson, Stephen P., Maystadt, Isabelle, Keren, Boris, Dixon, Joanne W., Skinner, Cindy, Stapleton, Rachel, Ruaud, Lyse, Gumus, Evren, Lakeman, Phillis, Alders, Mariëlle, Tedder, Matthew L., Schwartz, Charles E., Friez, Michael J., Sadikovic, Bekim, and Stevenson, Roger E.

Published
2023
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33. Functional correlation of genome-wide DNA methylation profiles in genetic neurodevelopmental disorders

Author

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

Subjects
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.

Published
2022

34. Novel diagnostic DNA methylation episignatures expand and refine the epigenetic landscapes of Mendelian disorders

Author

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

Subjects
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

35. Recurrent carotid paragangliomas in a syndromic patient with a heterozygous missense variant in DNA Methyltransferase 3 Alpha.

Author

German RJ, Vuocolo B, Vossaert L, Saba L, Fletcher R, Tedder ML, Sadikovic B, Kerkhof J, Wangler M, and Bacino CA

Abstract

We report a 40-year-old African American female with a novel variant in exon 8 of DNA methyltransferase 3 alpha (DNMT3A), (NM_022552.4: c.905G>C, p.G302A) who presented with a history of recurrent carotid paragangliomas, mediastinal mass, intellectual disability, dysarthria, cholelithiasis, diabetes mellitus, hypertension, and dysmorphic features. We interpret this novel variant as likely pathogenic and causative for the patient's syndromic features of Heyn-Sproul-Jackson syndrome. Heyn-Sproul-Jackson syndrome is a condition caused by gain-of-function genetic changes in DNMT3A. Paragangliomas have also been observed in non-syndromic patients with genetic alterations in DNMT3A. We describe a patient with clinical features of Heyn-Sproul-Jackson syndrome such as intellectual disability, dysarthria, brachydactyly, and lack of brain MRI findings to add evidence to associate paragangliomas with DNMT3A and draw particular attention to the potential involvement of the proline-tryptophan-tryptophan-proline domain of DNMT3A., (© 2024 Wiley Periodicals LLC.)

Published
2024
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36. Blepharophimosis with intellectual disability and Helsmoortel-Van Der Aa Syndrome share episignature and phenotype.

Author

Sarli C, van der Laan L, Reilly J, Trajkova S, Carli D, Brusco A, Levy MA, Relator R, Kerkhof J, McConkey H, Tedder ML, Skinner C, Alders M, Henneman P, Hennekam RCM, Ciaccio C, D'Arrigo S, Vitobello A, Faivre L, Weber S, Vincent-Devulder A, Perrin L, Bourgois A, Yamamoto T, Metcalfe K, Zollino M, Kini U, Oliveira D, Sousa SB, Williams D, Cappuccio G, Sadikovic B, and Brunetti-Pierri N

Abstract

Blepharophimosis with intellectual disability (BIS) is a recently recognized disorder distinct from Nicolaides-Baraister syndrome that presents with distinct facial features of blepharophimosis, developmental delay, and intellectual disability. BIS is caused by pathogenic variants in SMARCA2, that encodes the catalytic subunit of the superfamily II helicase group of the BRG1 and BRM-associated factors (BAF) forming the BAF complex, a chromatin remodeling complex involved in transcriptional regulation. Individuals bearing variants within the bipartite nuclear localization (BNL) signal domain of ADNP present with the neurodevelopmental disorder known as Helsmoortel-Van Der Aa Syndrome (HVDAS). Distinct DNA methylation profiles referred to as episignatures have been reported in HVDAS and BAF complex disorders. Due to molecular interactions between ADNP and BAF complex, and an overlapping craniofacial phenotype with narrowing of the palpebral fissures in a subset of patients with HVDAS and BIS, we hypothesized the possibility of a common phenotype-specific episignature. A distinct episignature was shared by 15 individuals with BIS-causing SMARCA2 pathogenic variants and 12 individuals with class II HVDAS caused by truncating pathogenic ADNP variants. This represents first evidence of a sensitive phenotype-specific episignature biomarker shared across distinct genetic conditions that also exhibit unique gene-specific episignatures., (© 2024 The Author(s). American Journal of Medical Genetics Part C: Seminars in Medical Genetics published by Wiley Periodicals LLC.)

Published
2024
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37. Diagnostic Utility of Genome-wide DNA Methylation Analysis in Genetically Unsolved Developmental and Epileptic Encephalopathies and Refinement of a CHD2 Episignature.

Author

LaFlamme CW, Rastin C, Sengupta S, Pennington HE, Russ-Hall SJ, Schneider AL, Bonkowski ES, Almanza Fuerte EP, Galey M, Goffena J, Gibson SB, Allan TJ, Nyaga DM, Lieffering N, Hebbar M, Walker EV, Darnell D, Olsen SR, Kolekar P, Djekidel N, Rosikiewicz W, McConkey H, Kerkhof J, Levy MA, Relator R, Lev D, Lerman-Sagie T, Park KL, Alders M, Cappuccio G, Chatron N, Demain L, Genevieve D, Lesca G, Roscioli T, Sanlaville D, Tedder ML, Hubshman MW, Ketkar S, Dai H, Worley KC, Rosenfeld JA, Chao HT, Neale G, Carvill GL, Wang Z, Berkovic SF, Sadleir LG, Miller DE, Scheffer IE, Sadikovic B, and Mefford HC

Abstract

Sequence-based genetic testing currently identifies causative genetic variants in ∼50% of individuals with developmental and epileptic encephalopathies (DEEs). Aberrant changes in DNA methylation are implicated in various neurodevelopmental disorders but remain unstudied in DEEs. Rare epigenetic variations ("epivariants") can drive disease by modulating gene expression at single loci, whereas genome-wide DNA methylation changes can result in distinct "episignature" biomarkers for monogenic disorders in a growing number of rare diseases. Here, we interrogate the diagnostic utility of genome-wide DNA methylation array analysis on peripheral blood samples from 516 individuals with genetically unsolved DEEs who had previously undergone extensive genetic testing. We identified rare differentially methylated regions (DMRs) and explanatory episignatures to discover causative and candidate genetic etiologies in 10 individuals. We then used long-read sequencing to identify DNA variants underlying rare DMRs, including one balanced translocation, three CG-rich repeat expansions, and two copy number variants. We also identify pathogenic sequence variants associated with episignatures; some had been missed by previous exome sequencing. Although most DEE genes lack known episignatures, the increase in diagnostic yield for DNA methylation analysis in DEEs is comparable to the added yield of genome sequencing. Finally, we refine an episignature for CHD2 using an 850K methylation array which was further refined at higher CpG resolution using bisulfite sequencing to investigate potential insights into CHD2 pathophysiology. Our study demonstrates the diagnostic yield of genome-wide DNA methylation analysis to identify causal and candidate genetic causes as ∼2% (10/516) for unsolved DEE cases.

Published
2023
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38. DNA methylation episignatures are sensitive and specific biomarkers for detection of patients with KAT6A / KAT6B variants.

Author

Vos N, Reilly J, Elting MW, Campeau PM, Coman D, Stark Z, Tan TY, Amor DJ, Kaur S, StJohn M, Morgan AT, Kamien BA, Patel C, Tedder ML, Merla G, Prontera P, Castori M, Muru K, Collins F, Christodoulou J, Smith J, Zeev BB, Murgia A, Leonardi E, Esber N, Martinez-Monseny A, Casas-Alba D, Wallis M, Mannens M, Levy MA, Relator R, Alders M, and Sadikovic B

Subjects
Humans, Biomarkers, Histone Acetyltransferases genetics, DNA Methylation, Neurodevelopmental Disorders genetics
Abstract

Accurate diagnosis for patients living with neurodevelopmental disorders is often met with numerous challenges, related to the ambiguity of findings and lack of specificity in genetic variants leading to pathology. Genome-wide DNA methylation analysis has been used to develop highly sensitive and specific 'episignatures' as biomarkers capable of differentiating and classifying complex neurodevelopmental disorders. In this study we describe distinct episignatures for KAT6A syndrome, caused by pathogenic variants in the lysine acetyltransferase A gene ( KAT6A ), and for the two neurodevelopmental disorders associated with lysine acetyl transferase B ( KAT6B ). We demonstrate the ability of our models to differentiate between highly overlapping episignatures, increasing the ability to effectively identify and diagnose these conditions.

Published
2023
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39. Novel diagnostic DNA methylation episignatures expand and refine the epigenetic landscapes of Mendelian disorders.

Author

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
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