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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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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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5. Menke-Hennekam syndrome; delineation of domain-specific subtypes with distinct clinical and DNA methylation profiles

Author

Angius, Andrea, Baker, Janice A., Bedoukian, Emma, Bhambhani, Vikas, Bodamer, Olaf, O’Brien, Alan, Clayton-Smith, Jill, Crisponi, Laura, Cueto González, Anna María, the DDD study, Devriendt, Koenraad, Garrido, Elena Dominguez, Ehmke, Nadja, van Eerde, Albertien, van den Elzen, Annette P.M., Faivre, Laurence, Fisher, Laura, Flores-Daboub, Josue A., Foster, Alison, Friedman, Jennifer, Gabau, Elisabeth, Galazzi, Elena, García-Miñaúr, Sixto, Garavelli, Livia, Gardeitchik, Thatjana, Gerkes, Erica H., van Gils, Julien, Giltay, Jacques C., Garcia, Aixa Gonzalez, Heimdal, Ketil Riddervold, Horn, Denise, Houge, Gunnar, Hufnagel, Sophia B., Ilencikova, Denisa, Julia, Sophie, Kant, Sarina G., Kinning, Esther, Klee, Eric W., Kois, Chelsea, Kovačević, Maja, Lachmeijer, A.M.A. (Guus), Lanpher, Brendan, Lebrun, Marine, Leon, Eyby, Lichty, Angie Ward, Lin, Ruth, Llano-Rivas, Isabel, Lynch, Sally Ann, Maas, Saskia M., Maitz, Silvia B., McKee, Shane, Melis, Daniela, Merati, Elisabetta, Merla, Giuseppe, Newbury-Ecob, Ruth, Nizon, Mathilde, Park, Soo-Mi, Patterson, Jennifer, Petit, Florence, Peeters, Hilde, Persani, Luca, Persico, Ivana, Pes, Valentina, Pollazzon, Marzia, Potjer, Thomas, Potocki, Lorraine, Pottinger, Carrie, Prasad, Chitra, Prijoles, Eloise J., Ragge, Nicola K., Rake, Jan Peter, van Ravenswaaij-Arts, Conny M.A., Rea, Gillian, Ruivenkamp, Claudia, Rutz, Audrey, Saitta, Sulagna C., Russo, Rossana Sanchez, Santen, Gijs W.E., Schaefer, Elise, Shashi, Vandana, Schultz-Rogers, Laura, Sluga, Andrea, Sotgiu, Stefano, Steichen-Gersdorf, Elisabeth, Sullivan, Jennifer A., Sun, Yu, Suri, Mohnish, Tartaglia, Marco, Tedder, Matt, Terhal, Paulien, Tully, Ian, Verbeek, Nienke, Wenzel, Maren, White, Susan M., Xiao, Bing, Haghshenas, Sadegheh, Bout, Hidde J., Schijns, Josephine M., Levy, Michael A., Kerkhof, Jennifer, Bhai, Pratibha, McConkey, Haley, Jenkins, Zandra A., Williams, Ella M., Halliday, Benjamin J., Huisman, Sylvia A., Lauffer, Peter, de Waard, Vivian, Witteveen, Laura, Banka, Siddharth, Brady, Angela F., Hurst, Anna C.E., Kaiser, Frank J., Lacombe, Didier, Martinez-Monseny, Antonio F., Fergelot, Patricia, Monteiro, Fabíola P., Parenti, Ilaria, Santos-Simarro, Fernando, Simpson, Brittany N., Alders, Mariëlle, Robertson, Stephen P., Sadikovic, Bekim, and Menke, Leonie A.

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. DNA methylation episignature, extension of the clinical features, and comparative epigenomic profiling of Hao-Fountain syndrome caused by variants in USP7

Author

van der Laan, Liselot, Karimi, Karim, Rooney, Kathleen, Lauffer, Peter, McConkey, Haley, Caro, Pilar, Relator, Raissa, Levy, Michael A., Bhai, Pratibha, Mignot, Cyril, Keren, Boris, Briuglia, Silvana, Sobering, Andrew K., Li, Dong, Vissers, Lisenka E.L.M., Dingemans, Alexander J.M., Valenzuela, Irene, Verberne, Eline A., Misra-Isrie, Mala, Zwijnenburg, Petra J.G., Waisfisz, Quinten, Alders, Mariëlle, Sailer, Sebastian, Schaaf, Christian P., Mannens, Marcel M.A.M., Sadikovic, Bekim, van Haelst, Mieke M., and Henneman, Peter

Published
2024
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8. 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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10. DNA methylation episignature and comparative epigenomic profiling of HNRNPU-related neurodevelopmental disorder

Author

Rooney, Kathleen, van der Laan, Liselot, Trajkova, Slavica, Haghshenas, Sadegheh, Relator, Raissa, Lauffer, Peter, Vos, Niels, Levy, Michael A., Brunetti-Pierri, Nicola, Terrone, Gaetano, Mignot, Cyril, Keren, Boris, de Villemeur, Thierry B., Volker-Touw, Catharina M.L., Verbeek, Nienke, van der Smagt, Jasper J., Oegema, Renske, Brusco, Alfredo, Ferrero, Giovanni B., Misra-Isrie, Mala, Hochstenbach, Ron, Alders, Mariëlle, Mannens, Marcel M.A.M., Sadikovic, Bekim, van Haelst, Mieke M., and Henneman, Peter

Published
2023
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11. Biallelic variants in the calpain regulatory subunit CAPNS1 cause pulmonary arterial hypertension

Author

Postma, Alex V., Rapp, Christina K., Knoflach, Katrin, Volk, Alexander E., Lemke, Johannes R., Ackermann, Maximilian, Regamey, Nicolas, Latzin, Philipp, Celant, Lucas, Jansen, Samara M.A., Bogaard, Harm J., Ilgun, Aho, Alders, Mariëlle, van Spaendonck-Zwarts, Karin Y., Jonigk, Danny, Klein, Christoph, Gräf, Stefan, Kubisch, Christian, Houweling, Arjan C., and Griese, Matthias

Published
2023
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12. NFIB Haploinsufficiency Is Associated with Intellectual Disability and Macrocephaly

Author

Schanze, Ina, Bunt, Jens, Lim, Jonathan WC, Schanze, Denny, Dean, Ryan J, Alders, Marielle, Blanchet, Patricia, Attié-Bitach, Tania, Berland, Siren, Boogert, Steven, Boppudi, Sangamitra, Bridges, Caitlin J, Cho, Megan T, Dobyns, William B, Donnai, Dian, Douglas, Jessica, Earl, Dawn L, Edwards, Timothy J, Faivre, Laurence, Fregeau, Brieana, Genevieve, David, Gérard, Marion, Gatinois, Vincent, Holder-Espinasse, Muriel, Huth, Samuel F, Izumi, Kosuke, Kerr, Bronwyn, Lacaze, Elodie, Lakeman, Phillis, Mahida, Sonal, Mirzaa, Ghayda M, Morgan, Sian M, Nowak, Catherine, Peeters, Hilde, Petit, Florence, Pilz, Daniela T, Puechberty, Jacques, Reinstein, Eyal, Rivière, Jean-Baptiste, Santani, Avni B, Schneider, Anouck, Sherr, Elliott H, Smith-Hicks, Constance, Wieland, Ilse, Zackai, Elaine, Zhao, Xiaonan, Gronostajski, Richard M, Zenker, Martin, and Richards, Linda J

Subjects
Biomedical and Clinical Sciences, Mental Health, Pediatric, Intellectual and Developmental Disabilities (IDD), Neurosciences, Rare Diseases, Behavioral and Social Science, Genetics, Brain Disorders, Aetiology, 2.1 Biological and endogenous factors, Mental health, Neurological, Adolescent, Adult, Animals, Cerebral Cortex, Child, Child, Preschool, Codon, Nonsense, Cohort Studies, Corpus Callosum, Female, Haploinsufficiency, Humans, Intellectual Disability, Male, Megalencephaly, Mice, Mice, Knockout, NFI Transcription Factors, Polymorphism, Single Nucleotide, Young Adult, NFIB, agenesis of the corpus callosum, chromosome 9p22.3, chromosome 9p23, developmental delay, haploinsufficiency, intellectual disability, macrocephaly, megalencephaly, nuclear factor I, Biological Sciences, Medical and Health Sciences, Genetics & Heredity, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

The nuclear factor I (NFI) family of transcription factors play an important role in normal development of multiple organs. Three NFI family members are highly expressed in the brain, and deletions or sequence variants in two of these, NFIA and NFIX, have been associated with intellectual disability (ID) and brain malformations. NFIB, however, has not previously been implicated in human disease. Here, we present a cohort of 18 individuals with mild ID and behavioral issues who are haploinsufficient for NFIB. Ten individuals harbored overlapping microdeletions of the chromosomal 9p23-p22.2 region, ranging in size from 225 kb to 4.3 Mb. Five additional subjects had point sequence variations creating a premature termination codon, and three subjects harbored single-nucleotide variations resulting in an inactive protein as determined using an in vitro reporter assay. All individuals presented with additional variable neurodevelopmental phenotypes, including muscular hypotonia, motor and speech delay, attention deficit disorder, autism spectrum disorder, and behavioral abnormalities. While structural brain anomalies, including dysgenesis of corpus callosum, were variable, individuals most frequently presented with macrocephaly. To determine whether macrocephaly could be a functional consequence of NFIB disruption, we analyzed a cortex-specific Nfib conditional knockout mouse model, which is postnatally viable. Utilizing magnetic resonance imaging and histology, we demonstrate that Nfib conditional knockout mice have enlargement of the cerebral cortex but preservation of overall brain structure and interhemispheric connectivity. Based on our findings, we propose that haploinsufficiency of NFIB causes ID with macrocephaly.

Published
2018

13. De Novo and Inherited Loss-of-Function Variants in TLK2: Clinical and Genotype-Phenotype Evaluation of a Distinct Neurodevelopmental Disorder

Author

Reijnders, Margot RF, Miller, Kerry A, Alvi, Mohsan, Goos, Jacqueline AC, Lees, Melissa M, de Burca, Anna, Henderson, Alex, Kraus, Alison, Mikat, Barbara, de Vries, Bert BA, Isidor, Bertrand, Kerr, Bronwyn, Marcelis, Carlo, Schluth-Bolard, Caroline, Deshpande, Charu, Ruivenkamp, Claudia AL, Wieczorek, Dagmar, Study, The Deciphering Developmental Disorders, Baralle, Diana, Blair, Edward M, Engels, Hartmut, Lüdecke, Hermann-Josef, Eason, Jacqueline, Santen, Gijs WE, Clayton-Smith, Jill, Chandler, Kate, Tatton-Brown, Katrina, Payne, Katelyn, Helbig, Katherine, Radtke, Kelly, Nugent, Kimberly M, Cremer, Kirsten, Strom, Tim M, Bird, Lynne M, Sinnema, Margje, Bitner-Glindzicz, Maria, van Dooren, Marieke F, Alders, Marielle, Koopmans, Marije, Brick, Lauren, Kozenko, Mariya, Harline, Megan L, Klaassens, Merel, Steinraths, Michelle, Cooper, Nicola S, Edery, Patrick, Yap, Patrick, Terhal, Paulien A, van der Spek, Peter J, Lakeman, Phillis, Taylor, Rachel L, Littlejohn, Rebecca O, Pfundt, Rolph, Mercimek-Andrews, Saadet, Stegmann, Alexander PA, Kant, Sarina G, McLean, Scott, Joss, Shelagh, Swagemakers, Sigrid MA, Douzgou, Sofia, Wall, Steven A, Küry, Sébastien, Calpena, Eduardo, Koelling, Nils, McGowan, Simon J, Twigg, Stephen RF, Mathijssen, Irene MJ, Nellaker, Christoffer, Brunner, Han G, and Wilkie, Andrew OM

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Genetics, Biotechnology, Brain Disorders, Human Genome, Neurosciences, Clinical Research, Aetiology, 2.1 Biological and endogenous factors, Adolescent, Adult, Base Sequence, Cell Line, Child, Child, Preschool, Facies, Female, Genetic Association Studies, Humans, Infant, Inheritance Patterns, Loss of Function Mutation, Male, Neurodevelopmental Disorders, Protein Kinases, RNA, Messenger, Translocation, Genetic, Young Adult, Deciphering Developmental Disorders Study, Tousled-like, facial averaging, haploinsufficiency, intellectual disability, kinase, Medical and Health Sciences, Genetics & Heredity, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Next-generation sequencing is a powerful tool for the discovery of genes related to neurodevelopmental disorders (NDDs). Here, we report the identification of a distinct syndrome due to de novo or inherited heterozygous mutations in Tousled-like kinase 2 (TLK2) in 38 unrelated individuals and two affected mothers, using whole-exome and whole-genome sequencing technologies, matchmaker databases, and international collaborations. Affected individuals had a consistent phenotype, characterized by mild-borderline neurodevelopmental delay (86%), behavioral disorders (68%), severe gastro-intestinal problems (63%), and facial dysmorphism including blepharophimosis (82%), telecanthus (74%), prominent nasal bridge (68%), broad nasal tip (66%), thin vermilion of the upper lip (62%), and upslanting palpebral fissures (55%). Analysis of cell lines from three affected individuals showed that mutations act through a loss-of-function mechanism in at least two case subjects. Genotype-phenotype analysis and comparison of computationally modeled faces showed that phenotypes of these and other individuals with loss-of-function variants significantly overlapped with phenotypes of individuals with other variant types (missense and C-terminal truncating). This suggests that haploinsufficiency of TLK2 is the most likely underlying disease mechanism, leading to a consistent neurodevelopmental phenotype. This work illustrates the power of international data sharing, by the identification of 40 individuals from 26 different centers in 7 different countries, allowing the identification, clinical delineation, and genotype-phenotype evaluation of a distinct NDD caused by mutations in TLK2.

Published
2018

14. 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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15. Refining the 9q34.3 microduplication syndrome reveals mild neurodevelopmental features associated with a distinct global DNA methylation profile

Author

Rots, Dmitrijs, Rooney, Kathleen, Relator, Raissa, Kerkhof, Jennifer, Mcconkey, Haley, Pfundt, Rolph, Marcelis, Carlo, Willemsen, Marjolein H., van Hagen, Johanna M., Zwijnenburg, Petra, Alders, Marielle, Ounap, Katrin, Reimand, Tiia, Fjodorova, Olga, Berland, Siren, Liahjell, Eva Benedicte, Bojovic, Ognjen, Kriek, Marjolein, Ruivenkamp, Claudia, Bonati, Maria Teresa, Brunner, Han G., Vissers, Lisenka E. L. M., Sadikovic, Bekim, Kleefstra, Tjitske, Rots, Dmitrijs, Rooney, Kathleen, Relator, Raissa, Kerkhof, Jennifer, Mcconkey, Haley, Pfundt, Rolph, Marcelis, Carlo, Willemsen, Marjolein H., van Hagen, Johanna M., Zwijnenburg, Petra, Alders, Marielle, Ounap, Katrin, Reimand, Tiia, Fjodorova, Olga, Berland, Siren, Liahjell, Eva Benedicte, Bojovic, Ognjen, Kriek, Marjolein, Ruivenkamp, Claudia, Bonati, Maria Teresa, Brunner, Han G., Vissers, Lisenka E. L. M., Sadikovic, Bekim, and Kleefstra, Tjitske

Abstract

Precise regulation of gene expression is important for correct neurodevelopment. 9q34.3 deletions affecting the EHMT1 gene result in a syndromic neurodevelopmental disorder named Kleefstra syndrome. In contrast, duplications of the 9q34.3 locus encompassing EHMT1 have been suggested to cause developmental disorders, but only limited information has been available. We have identified 15 individuals from 10 unrelated families, with 9q34.3 duplications <1.5 Mb in size, encompassing EHMT1 entirely. Clinical features included mild developmental delay, mild intellectual disability or learning problems, autism spectrum disorder, and behavior problems. The individuals did not consistently display dysmorphic features, congenital anomalies, or growth abnormalities. DNA methylation analysis revealed a weak DNAm profile for the cases with 9q34.3 duplication encompassing EHMT1, which could segregate the majority of the affected cases from controls. This study shows that individuals with 9q34.3 duplications including EHMT1 gene present with mild non-syndromic neurodevelopmental disorders and DNA methylation changes different from Kleefstra syndrome.

Published
2024

16. Dihydropyrimidine Dehydrogenase Deficiency: Homozygosity for an Extremely Rare Variant in DPYD due to Uniparental Isodisomy of Chromosome 1

Author

van Kuilenburg, André B. P., Meijer, Judith, Meinsma, Rutger, Pérez-Dueñas, Belén, Alders, Marielle, Bhuiyan, Zahurul A., Artuch, Rafael, Hennekam, Raoul C. M., Baumgartner, Matthias, Series Editor, Patterson, Marc, Series Editor, Rahman, Shamima, Series Editor, Peters, Verena, Series Editor, Morava, Eva, Editor-in-Chief, and Zschocke, Johannes, Series Editor

Published
2019
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17. Deficiency of TET3 leads to a genome-wide DNA hypermethylation episignature in human whole blood

Author

Levy, Michael A., Beck, David B., Metcalfe, Kay, Douzgou, Sofia, Sithambaram, Sivagamy, Cottrell, Trudie, Ansar, Muhammad, Kerkhof, Jennifer, Mignot, Cyril, Nougues, Marie-Christine, Keren, Boris, Moore, Hannah W., Oegema, Renske, Giltay, Jacques C., Simon, Marleen, van Jaarsveld, Richard H., Bos, Jessica, van Haelst, Mieke, Motazacker, M. Mahdi, Boon, Elles M. J., Santen, Gijs W. E., Ruivenkamp, Claudia A. L., Alders, Marielle, Luperchio, Teresa Romeo, Boukas, Leandros, Ramsey, Keri, Narayanan, Vinodh, Schaefer, G. Bradley, Bonasio, Roberto, Doheny, Kimberly F., Stevenson, Roger E., Banka, Siddharth, Sadikovic, Bekim, and Fahrner, Jill A.

Published
2021
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18. DNA methylation episignature and comparative epigenomic profiling for Pitt-Hopkins syndrome caused by TCF4 variants

Author

van der Laan, Liselot, Lauffer, Peter, Rooney, Kathleen, Silva, Ananília, Haghshenas, Sadegheh, Relator, Raissa, Levy, Michael A., Trajkova, Slavica, Huisman, Sylvia A., Bijlsma, Emilia K., Kleefstra, Tjitske, van Bon, Bregje W., Baysal, Özlem, Zweier, Christiane, Palomares-Bralo, María, Fischer, Jan, Szakszon, Katalin, Faivre, Laurence, Piton, Amélie, Mesman, Simone, Hochstenbach, Ron, Elting, Mariet W., van Hagen, Johanna M., Plomp, Astrid S., Mannens, Marcel M.A.M., Alders, Mariëlle, van Haelst, Mieke M., Ferrero, Giovanni B., Brusco, Alfredo, Henneman, Peter, Sweetser, David A., Sadikovic, Bekim, Vitobello, Antonio, and Menke, Leonie A.

Published
2024
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19. Transcription alterations of KCNQ1 associated with imprinted methylation defects in the Beckwith–Wiedemann locus

Author

Valente, Federica Maria, Sparago, Angela, Freschi, Andrea, Hill-Harfe, Katherine, Maas, Saskia M., Frints, Suzanna Gerarda Maria, Alders, Marielle, Pignata, Laura, Franzese, Monica, Angelini, Claudia, Carli, Diana, Mussa, Alessandro, Gazzin, Andrea, Gabbarini, Fulvio, Acurzio, Basilia, Ferrero, Giovanni Battista, Bliek, Jet, Williams, Charles A., Riccio, Andrea, and Cerrato, Flavia

Published
2019
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20. 5q35 duplication syndrome:Narrowing the critical region on the distal side and further evidence of intrafamilial variability and expression

Author

van der Lugt, Neeltje Margreth, Weerts, Marjolein J.A., Veenma, Danielle C.M., Lincke, Carsten R., Gischler, Saskia J., Alders, Marielle, van Ierland, Yvette, van der Lugt, Neeltje Margreth, Weerts, Marjolein J.A., Veenma, Danielle C.M., Lincke, Carsten R., Gischler, Saskia J., Alders, Marielle, and van Ierland, Yvette

Abstract

The key features of patients with a microduplication 5q35.2q35.3 (including the NSD1 gene) are short stature, microcephaly, mild developmental delay, behavioral problems, digital anomalies and congenital anomalies of internal organs. This core phenotype can be viewed as the reversed phenotype of Sotos syndrome, which is caused by a microdeletion in the same chromosomal region or a pathogenic variant in the NSD1 gene, and includes tall stature and macrocephaly, developmental delay, and epilepsy. Here, we report on a patient and his mother, both with a 5q35.2q35.3 duplication, adding a fifth family to the recently published overview of 39 patients of Quintero-Rivera et al. Our patient had several congenital anomalies, intrauterine growth restriction with a persisting short stature, while his mother was only mildly affected with decreased growth parameters. In addition, he had hemophagogocytic lymphohistiocytosis (HLH) triggered by Haemophilus influenzae and was recently diagnosed with Ewing sarcoma. Our cases carry the smallest duplication published (ca 332 kb, arr[hg19] 5q35.2q35.3(176493106-176824785)x3) further narrowing the distal side of the critical region of the 5q35.2q35.3 duplication. Besides broadening the clinical phenotypic spectrum, our report indicates that the 5q35.2q35.3 microduplication also shows a large intra-familial variability and expression.

Published
2023

21. Lymphedema as first clinical presentation of Cantu Syndrome: reversed phenotyping after identification of gain-of-function variant in ABCC9

Author

Genetica Klinische Genetica, Genetica, Genetica Sectie Research, Cancer, Child Health, Gao, Jian, McClenaghan, Conor, Christiaans, Imke, Alders, Marielle, van Duinen, Kirsten, van Haelst, Mieke M., van Haaften, Gijs, Nichols, Colin G., Genetica Klinische Genetica, Genetica, Genetica Sectie Research, Cancer, Child Health, Gao, Jian, McClenaghan, Conor, Christiaans, Imke, Alders, Marielle, van Duinen, Kirsten, van Haelst, Mieke M., van Haaften, Gijs, and Nichols, Colin G.

Published
2023

22. 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

27. 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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28. De novo variants in genes regulating stress granule assembly associate with neurodevelopmental disorders

Author

Jia, Xiangbin, primary, Zhang, Shujie, additional, Tan, Senwei, additional, Du, Bing, additional, He, Mei, additional, Qin, Haisong, additional, Chen, Jia, additional, Duan, Xinyu, additional, Luo, Jingsi, additional, Chen, Fei, additional, Ouyang, Luping, additional, Wang, Jian, additional, Chen, Guodong, additional, Yu, Bin, additional, Zhang, Ge, additional, Zhang, Zimin, additional, Lyu, Yongqing, additional, Huang, Yi, additional, Jiao, Jian, additional, Chen, Jin Yun (Helen), additional, Swoboda, Kathryn J., additional, Agolini, Emanuele, additional, Novelli, Antonio, additional, Leoni, Chiara, additional, Zampino, Giuseppe, additional, Cappuccio, Gerarda, additional, Brunetti-Pierri, Nicola, additional, Gerard, Benedicte, additional, Ginglinger, Emmanuelle, additional, Richer, Julie, additional, McMillan, Hugh, additional, White-Brown, Alexandre, additional, Hoekzema, Kendra, additional, Bernier, Raphael A., additional, Kurtz-Nelson, Evangeline C., additional, Earl, Rachel K., additional, Meddens, Claartje, additional, Alders, Marielle, additional, Fuchs, Meredith, additional, Caumes, Roseline, additional, Brunelle, Perrine, additional, Smol, Thomas, additional, Kuehl, Ryan, additional, Day-Salvatore, Debra-Lynn, additional, Monaghan, Kristin G., additional, Morrow, Michelle M., additional, Eichler, Evan E., additional, Hu, Zhengmao, additional, Yuan, Ling, additional, Tan, Jieqiong, additional, Xia, Kun, additional, Shen, Yiping, additional, and Guo, Hui, additional

Published
2022
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29. De novo variants in the PABP domain of PABPC1 lead to developmental delay

Author

Wegler, Meret, primary, Jia, Xiangbin, additional, Alders, Marielle, additional, Bouman, Arjan, additional, Chen, Jia, additional, Duan, Xinyu, additional, Lauzon, Julie L., additional, Mathijssen, Inge B., additional, Sticht, Heinrich, additional, Syrbe, Steffen, additional, Tan, Senwei, additional, Guo, Hui, additional, and Abou Jamra, Rami, additional

Published
2022
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34. 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

35. 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

36. 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

38. 5q35 duplication syndrome: Narrowing the critical region on the distal side and further evidence of intrafamilial variability and expression.

Author

van der Lugt, Neeltje Margreth, Weerts, Marjolein J. A., Veenma, Danielle C. M., Lincke, Carsten R., Gischler, Saskia J., Alders, Marielle, and van Ierland, Yvette

Abstract

The key features of patients with a microduplication 5q35.2q35.3 (including the NSD1 gene) are short stature, microcephaly, mild developmental delay, behavioral problems, digital anomalies and congenital anomalies of internal organs. This core phenotype can be viewed as the reversed phenotype of Sotos syndrome, which is caused by a microdeletion in the same chromosomal region or a pathogenic variant in the NSD1 gene, and includes tall stature and macrocephaly, developmental delay, and epilepsy. Here, we report on a patient and his mother, both with a 5q35.2q35.3 duplication, adding a fifth family to the recently published overview of 39 patients of Quintero‐Rivera et al. Our patient had several congenital anomalies, intrauterine growth restriction with a persisting short stature, while his mother was only mildly affected with decreased growth parameters. In addition, he had hemophagogocytic lymphohistiocytosis (HLH) triggered by Haemophilus influenzae and was recently diagnosed with Ewing sarcoma. Our cases carry the smallest duplication published (ca 332 kb, arr[hg19] 5q35.2q35.3(176493106‐176824785)x3) further narrowing the distal side of the critical region of the 5q35.2q35.3 duplication. Besides broadening the clinical phenotypic spectrum, our report indicates that the 5q35.2q35.3 microduplication also shows a large intra‐familial variability and expression. [ABSTRACT FROM AUTHOR]

Published
2023
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41. Author Correction: Deficiency of TET3 leads to a genome-wide DNA hypermethylation episignature in human whole blood (npj Genomic Medicine, (2021), 6, 1, (92), 10.1038/s41525-021-00256-y)

Author

Levy, Michael A., Beck, David B., Metcalfe, Kay, Douzgou, Sofia, Sithambaram, Sivagamy, Cottrell, Trudie, Ansar, Muhammad, Kerkhof, Jennifer, Mignot, Cyril, Nougues, Marie-Christine, Keren, Boris, Moore, Hannah W., Oegema, Renske, Giltay, Jacques C., Simon, Marleen, van Jaarsveld, Richard H., Bos, Jessica, van Haelst, Mieke, Motazacker, M. Mahdi, Boon, Elles M. J., Santen, Gijs W. E., Ruivenkamp, Claudia A. L., Alders, Marielle, Luperchio, Teresa Romeo, Boukas, Leandros, Ramsey, Keri, Narayanan, Vinodh, Schaefer, G. Bradley, Bonasio, Roberto, Doheny, Kimberly F., Stevenson, Roger E., Banka, Siddharth, Sadikovic, Bekim, Fahrner, Jill A., Human Genetics, ACS - Pulmonary hypertension & thrombosis, Amsterdam Neuroscience - Complex Trait Genetics, Amsterdam Reproduction & Development (AR&D), and Human genetics

Abstract

In this article the author name Siddharth Banka was incorrectly written as Sidharth Banka. The original article has been corrected.

Published
2021

42. Author Correction: Deficiency of TET3 leads to a genome-wide DNA hypermethylation episignature in human whole blood (npj Genomic Medicine, (2021), 6, 1, (92), 10.1038/s41525-021-00256-y):Deficiency of TET3 leads to a genome-wide DNA hypermethylation episignature in human whole blood (npj Genomic Medicine, (2021), 6, 1, (92), 10.1038/s41525-021-00256-y)

Author

Levy, Michael A, Beck, David B, Metcalfe, Kay, Douzgou, Sofia, Sithambaram, Sivagamy, Cottrell, Trudie, Ansar, Muhammad, Kerkhof, Jennifer, Mignot, Cyril, Nougues, Marie-Christine, Keren, Boris, Moore, Hannah W, Oegema, Renske, Giltay, Jacques C, Simon, Marleen, van Jaarsveld, Richard H, Bos, Jessica, van Haelst, Mieke, Motazacker, M Mahdi, Boon, Elles M J, Santen, Gijs W E, Ruivenkamp, Claudia A L, Alders, Marielle, Luperchio, Teresa Romeo, Boukas, Leandros, Ramsey, Keri, Narayanan, Vinodh, Schaefer, G Bradley, Bonasio, Roberto, Doheny, Kimberly F, Stevenson, Roger E, Banka, Siddharth, Sadikovic, Bekim, and Fahrner, Jill A

Abstract

In this article the author name Siddharth Banka was incorrectly written as Sidharth Banka. The original article has been corrected.

Published
2021

43. 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

44. 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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45. Delineating the molecular and phenotypic spectrum of the SETD1B-related syndrome

Author

Weerts, Marjolein J.A., primary, Lanko, Kristina, additional, Guzmán-Vega, Francisco J., additional, Jackson, Adam, additional, Ramakrishnan, Reshmi, additional, Cardona-Londoño, Kelly J., additional, Peña-Guerra, Karla A., additional, van Bever, Yolande, additional, van Paassen, Barbara W., additional, Kievit, Anneke, additional, van Slegtenhorst, Marjon, additional, Allen, Nicholas M., additional, Kehoe, Caroline M., additional, Robinson, Hannah K., additional, Pang, Lewis, additional, Banu, Selina H., additional, Zaman, Mashaya, additional, Efthymiou, Stephanie, additional, Houlden, Henry, additional, Järvelä, Irma, additional, Lauronen, Leena, additional, Määttä, Tuomo, additional, Schrauwen, Isabelle, additional, Leal, Suzanne M., additional, Ruivenkamp, Claudia A.L., additional, Barge-Schaapveld, Daniela Q.C.M., additional, Peeters-Scholte, Cacha M.P.C.D., additional, Galehdari, Hamid, additional, Mazaheri, Neda, additional, Sisodiya, Sanjay M., additional, Harrison, Victoria, additional, Sun, Angela, additional, Thies, Jenny, additional, Pedroza, Luis Alberto, additional, Lara-Taranchenko, Yana, additional, Chinn, Ivan K., additional, Lupski, James R., additional, Garza-Flores, Alexandra, additional, McGlothlin, Jeffery, additional, Yang, Lin, additional, Huang, Shaoping, additional, Wang, Xiaodong, additional, Jewett, Tamison, additional, Rosso, Gretchen, additional, Lin, Xi, additional, Mohammed, Shehla, additional, Merritt, J. Lawrence, additional, Mirzaa, Ghayda M., additional, Timms, Andrew E., additional, Scheck, Joshua, additional, Elting, Mariet W., additional, Polstra, Abeltje M., additional, Schenck, Lauren, additional, Ruzhnikov, Maura R.Z., additional, Vetro, Annalisa, additional, Montomoli, Martino, additional, Guerrini, Renzo, additional, Koboldt, Daniel C., additional, Mosher, Theresa Mihalic, additional, Pastore, Matthew T., additional, McBride, Kim L., additional, Peng, Jing, additional, Pan, Zou, additional, Willemsen, Marjolein, additional, Koning, Susanne, additional, Turnpenny, Peter D., additional, de Vries, Bert B.A., additional, Gilissen, Christian, additional, Pfundt, Rolph, additional, Lees, Melissa, additional, Braddock, Stephen R., additional, Klemp, Kara C., additional, Vansenne, Fleur, additional, van Gijn, Marielle E., additional, Quindipan, Catherine, additional, Deardorff, Matthew A., additional, Hamm, J. Austin, additional, Putnam, Abbey M., additional, Baud, Rebecca, additional, Walsh, Laurence, additional, Lynch, Sally A., additional, Baptista, Julia, additional, Person, Richard E., additional, Monaghan, Kristin G., additional, Crunk, Amy, additional, Keller-Ramey, Jennifer, additional, Reich, Adi, additional, Elloumi, Houda Zghal, additional, Alders, Marielle, additional, Kerkhof, Jennifer, additional, McConkey, Haley, additional, Haghshenas, Sadegheh, additional, Maroofian, Reza, additional, Sadikovic, Bekim, additional, Banka, Siddharth, additional, Arold, Stefan T., additional, and Barakat, Tahsin Stefan, additional

Published
2021
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48. An international compendium of mutations in the SCN5A-encoded cardiac sodium channel in patients referred for Brugada syndrome genetic testing

Author

Kapplinger, Jamie D., Tester, David J., Alders, Marielle, Benito, Begoña, Berthet, Myriam, Brugada, Josep, Brugada, Pedro, Fressart, Véronique, Guerchicoff, Alejandra, Harris-Kerr, Carole, Kamakura, Shiro, Kyndt, Florence, Koopmann, Tamara T., Miyamoto, Yoshihiro, Pfeiffer, Ryan, Pollevick, Guido D., Probst, Vincent, Zumhagen, Sven, Vatta, Matteo, Towbin, Jeffrey A., Shimizu, Wataru, Schulze-Bahr, Eric, Antzelevitch, Charles, Salisbury, Benjamin A., Guicheney, Pascale, Wilde, Arthur A.M., Brugada, Ramon, Schott, Jean-Jacques, and Ackerman, Michael J.

Published
2010
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50. Author Correction: Deficiency of TET3 leads to a genome-wide DNA hypermethylation episignature in human whole blood

Author

Genetica Klinische Genetica, Brain, Child Health, Genetica Sectie Genoomdiagnostiek, Levy, Michael A, Beck, David B, Metcalfe, Kay, Douzgou, Sofia, Sithambaram, Sivagamy, Cottrell, Trudie, Ansar, Muhammad, Kerkhof, Jennifer, Mignot, Cyril, Nougues, Marie-Christine, Keren, Boris, Moore, Hannah W, Oegema, Renske, Giltay, Jacques C, Simon, Marleen, van Jaarsveld, Richard H, Bos, Jessica, van Haelst, Mieke, Motazacker, M Mahdi, Boon, Elles M J, Santen, Gijs W E, Ruivenkamp, Claudia A L, Alders, Marielle, Luperchio, Teresa Romeo, Boukas, Leandros, Ramsey, Keri, Narayanan, Vinodh, Schaefer, G Bradley, Bonasio, Roberto, Doheny, Kimberly F, Stevenson, Roger E, Banka, Siddharth, Sadikovic, Bekim, Fahrner, Jill A, Genetica Klinische Genetica, Brain, Child Health, Genetica Sectie Genoomdiagnostiek, Levy, Michael A, Beck, David B, Metcalfe, Kay, Douzgou, Sofia, Sithambaram, Sivagamy, Cottrell, Trudie, Ansar, Muhammad, Kerkhof, Jennifer, Mignot, Cyril, Nougues, Marie-Christine, Keren, Boris, Moore, Hannah W, Oegema, Renske, Giltay, Jacques C, Simon, Marleen, van Jaarsveld, Richard H, Bos, Jessica, van Haelst, Mieke, Motazacker, M Mahdi, Boon, Elles M J, Santen, Gijs W E, Ruivenkamp, Claudia A L, Alders, Marielle, Luperchio, Teresa Romeo, Boukas, Leandros, Ramsey, Keri, Narayanan, Vinodh, Schaefer, G Bradley, Bonasio, Roberto, Doheny, Kimberly F, Stevenson, Roger E, Banka, Siddharth, Sadikovic, Bekim, and Fahrner, Jill A

Published
2021

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