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180 results on '"Ruivenkamp, C."'

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

Author

Rots, D., Rooney, K., Relator, R., Kerkhof, J., McConkey, H., Pfundt, R.P., Marcelis, C.L.M., Willemsen, M.H., Hagen, J.M. van, Zwijnenburg, P., Alders, M., Õunap, K., Reimand, T., Fjodorova, O., Berland, S., Liahjell, E.B., Bojovic, O., Kriek, M., Ruivenkamp, C., Bonati, M.T., Brunner, H.G., Vissers, L.E.L.M., Sadikovic, B., Kleefstra, T., Rots, D., Rooney, K., Relator, R., Kerkhof, J., McConkey, H., Pfundt, R.P., Marcelis, C.L.M., Willemsen, M.H., Hagen, J.M. van, Zwijnenburg, P., Alders, M., Õunap, K., Reimand, T., Fjodorova, O., Berland, S., Liahjell, E.B., Bojovic, O., Kriek, M., Ruivenkamp, C., Bonati, M.T., Brunner, H.G., Vissers, L.E.L.M., Sadikovic, B., and Kleefstra, T.

Abstract

Contains fulltext : 306427.pdf (Publisher’s version ) (Open Access), 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., 01 juni 2024

Published
2024

2. A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Author

Denomme-Pichon A. -S., Bruel A. -L., Duffourd Y., Safraou H., Thauvin-Robinet C., Tran Mau-Them F., Philippe C., Vitobello A., Jean-Marcais N., Moutton S., Thevenon J., Faivre L., Matalonga L., de Boer E., Gilissen C., Hoischen A., Kleefstra T., Pfundt R., de Vries B. B. A., Willemsen M. H., Vissers L. E. L. M., Jackson A., Banka S., Clayton-Smith J., Benetti E., Fallerini C., Renieri A., Ciolfi A., Dallapiccola B., Pizzi S., Radio F. C., Tartaglia M., Ellwanger K., Graessner H., Haack T. B., Zurek B., Havlovicova M., Macek M., Ryba L., Schwarz M., Votypka P., Lopez-Martin E., Posada M., Mencarelli M. A., Rooryck C., Trimouille A., Verloes A., Abbott K. M., Kerstjens M., Martin E. L., Maystadt I., Morleo M., Nigro V., Pinelli M., Riess O., Agathe J. -M. D. S., Santen G. W. E., Thauvin C., Torella A., Vissers L., Zguro K., Boer E. D., Cohen E., Danis D., Gao F., Horvath R., Johari M., Johanson L., Li S., Morsy H., Nelson I., Paramonov I., te Paske I. B. A. W., Robinson P., Savarese M., Steyaert W., Topf A., van der Velde J. K., Vandrovcova J., Ossowski S., Demidov G., Sturm M., Schulze-Hentrich J. M., Schule R., Xu J., Kessler C., Wayand M., Synofzik M., Wilke C., Traschutz A., Schols L., Hengel H., Lerche H., Kegele J., Heutink P., Brunner H., Scheffer H., Hoogerbrugge N., 't Hoen P. A. C., Sablauskas K., de Voer R. M., Kamsteeg E. -J., van de Warrenburg B., van Os N., Paske I. T., Janssen E., Steehouwer M., Yaldiz B., Brookes A. J., Veal C., Gibson S., Maddi V., Mehtarizadeh M., Riaz U., Warren G., Dizjikan F. Y., Shorter T., Straub V., Bettolo C. M., Manera J. D., Hambleton S., Engelhardt K., Alexander E., Peyron C., Pelissier A., Beltran S., Gut I. G., Laurie S., Piscia D., Papakonstantinou A., Bullich G., Corvo A., Fernandez-Callejo M., Hernandez C., Pico D., Lochmuller H., Gumus G., Bros-Facer V., Rath A., Hanauer M., Lagorce D., Hongnat O., Chahdil M., Lebreton E., Stevanin G., Durr A., Davoine C. -S., Guillot-Noel L., Heinzmann A., Coarelli G., Bonne G., Evangelista T., Allamand V., Ben Yaou R., Metay C., Eymard B., Atalaia A., Stojkovic T., Turnovec M., Thomasova D., Kremlikova R. P., Frankova V., Liskova P., Dolezalova P., Parkinson H., Keane T., Freeberg M., Thomas C., Spalding D., Robert G., Costa A., Patch C., Hanna M., Houlden H., Reilly M., Efthymiou S., Cali E., Magrinelli F., Sisodiya S. M., Rohrer J., Muntoni F., Zaharieva I., Sarkozy A., Timmerman V., Baets J., de Vries G., De Winter J., Beijer D., de Jonghe P., Van de Vondel L., De Ridder W., Weckhuysen S., Mutarelli M., Varavallo A., Banfi S., Musacchia F., Piluso G., Ferlini A., Selvatici R., Gualandi F., Bigoni S., Rossi R., Neri M., Aretz S., Spier I., Sommer A. K., Peters S., Oliveira C., Pelaez J. G., Matos A. R., Jose C. S., Ferreira M., Gullo I., Fernandes S., Garrido L., Ferreira P., Carneiro F., Swertz M. A., Johansson L., van der Vries G., Neerincx P. B., Ruvolo D., Kerstjens Frederikse W. S., Zonneveld-Huijssoon E., Roelofs-Prins D., van Gijn M., Kohler S., Metcalfe A., Drunat S., Heron D., Mignot C., Keren B., Lacombe D., Capella G., Valle L., Holinski-Feder E., Laner A., Steinke-Lange V., Cilio M. -R., Carpancea E., Depondt C., Lederer D., Sznajer Y., Duerinckx S., Mary S., Macaya A., Cazurro-Gutierrez A., Perez-Duenas B., Munell F., Jarava C. F., Maso L. B., Marce-Grau A., Colobran R., Hackman P., Udd B., Hemelsoet D., Dermaut B., Schuermans N., Poppe B., Verdin H., Osorio A. N., Depienne C., Roos A., Cordts I., Deschauer M., Striano P., Zara F., Riva A., Iacomino M., Uva P., Scala M., Scudieri P., Basak A. N., Claeys K., Boztug K., Haimel M., W. E G., Ruivenkamp C. A. L., Natera de Benito D., Thompson R., Polavarapu K., Grimbacher B., Zaganas I., Kokosali E., Lambros M., Evangeliou A., Spilioti M., Kapaki E., Bourbouli M., Balicza P., Molnar M. J., De la Paz M. P., Sanchez E. B., Delgado B. M., Alonso Garcia de la Rosa F. J., Schrock E., Rump A., Mei D., Vetro A., Balestrini S., Guerrini R., Chinnery P. F., Ratnaike T., Schon K., Maver A., Peterlin B., Munchau A., Lohmann K., Herzog R., Pauly M., May P., Beeson D., Cossins J., Furini S., Afenjar A., Goldenberg A., Masurel A., Phan A., Dieux-Coeslier A., Fargeot A., Guerrot A. -M., Toutain A., Molin A., Sorlin A., Putoux A., Jouret B., Laudier B., Demeer B., Doray B., Bonniaud B., Isidor B., Gilbert-Dussardier B., Leheup B., Reversade B., Paul C., Vincent-Delorme C., Neiva C., Poirsier C., Quelin C., Chiaverini C., Coubes C., Francannet C., Colson C., Desplantes C., Wells C., Goizet C., Sanlaville D., Amram D., Lehalle D., Genevieve D., Gaillard D., Zivi E., Sarrazin E., Steichen E., Schaefer E., Lacaze E., Jacquemin E., Bongers E., Kilic E., Colin E., Giuliano F., Prieur F., Laffargue F., Morice-Picard F., Petit F., Cartault F., Feillet F., Baujat G., Morin G., Diene G., Journel H., Perthus I., Lespinasse J., Alessandri J. -L., Amiel J., Martinovic J., Delanne J., Albuisson J., Lambert L., Perrin L., Ousager L. B., Van Maldergem L., Pinson L., Ruaud L., Samimi M., Bournez M., Bonnet-Dupeyron M. N., Vincent M., Jacquemont M. -L., Cordier-Alex M. -P., Gerard-Blanluet M., Willems M., Spodenkiewicz M., Doco-Fenzy M., Rossi M., Renaud M., Fradin M., Mathieu M., Holder-Espinasse M. H., Houcinat N., Hanna N., Leperrier N., Chassaing N., Philip N., Boute O., Van Kien P. K., Parent P., Bitoun P., Sarda P., Vabres P., Jouk P. -S., Touraine R., El Chehadeh S., Whalen S., Marlin S., Passemard S., Grotto S., Bellanger S. A., Blesson S., Nambot S., Naudion S., Lyonnet S., Odent S., Attie-Bitach T., Busa T., Drouin-Garraud V., Layet V., Bizaoui V., Cusin V., Capri Y., Alembik Y., Unión Europea. Comisión Europea. H2020, Unión Europea. Comisión Europea. 7 Programa Marco, Instituto de Salud Carlos III, Instituto Nacional de Bioinformatica (España), Ministry of Health (República Checa), Ministry of Education, Youth and Sports (República Checa), Denomme-Pichon, A. -S., Bruel, A. -L., Duffourd, Y., Safraou, H., Thauvin-Robinet, C., Tran Mau-Them, F., Philippe, C., Vitobello, A., Jean-Marcais, N., Moutton, S., Thevenon, J., Faivre, L., Matalonga, L., de Boer, E., Gilissen, C., Hoischen, A., Kleefstra, T., Pfundt, R., de Vries, B. B. A., Willemsen, M. H., Vissers, L. E. L. M., Jackson, A., Banka, S., Clayton-Smith, J., Benetti, E., Fallerini, C., Renieri, A., Ciolfi, A., Dallapiccola, B., Pizzi, S., Radio, F. C., Tartaglia, M., Ellwanger, K., Graessner, H., Haack, T. B., Zurek, B., Havlovicova, M., Macek, M., Ryba, L., Schwarz, M., Votypka, P., Lopez-Martin, E., Posada, M., Mencarelli, M. A., Rooryck, C., Trimouille, A., Verloes, A., Abbott, K. M., Kerstjens, M., Martin, E. L., Maystadt, I., Morleo, M., Nigro, V., Pinelli, M., Riess, O., Agathe, J. -M. D. S., Santen, G. W. E., Thauvin, C., Torella, A., Vissers, L., Zguro, K., Boer, E. D., Cohen, E., Danis, D., Gao, F., Horvath, R., Johari, M., Johanson, L., Li, S., Morsy, H., Nelson, I., Paramonov, I., te Paske, I. B. A. W., Robinson, P., Savarese, M., Steyaert, W., Topf, A., van der Velde, J. K., Vandrovcova, J., Ossowski, S., Demidov, G., Sturm, M., Schulze-Hentrich, J. M., Schule, R., Xu, J., Kessler, C., Wayand, M., Synofzik, M., Wilke, C., Traschutz, A., Schols, L., Hengel, H., Lerche, H., Kegele, J., Heutink, P., Brunner, H., Scheffer, H., Hoogerbrugge, N., 't Hoen, P. A. C., Sablauskas, K., de Voer, R. M., Kamsteeg, E. -J., van de Warrenburg, B., van Os, N., Paske, I. T., Janssen, E., Steehouwer, M., Yaldiz, B., Brookes, A. J., Veal, C., Gibson, S., Maddi, V., Mehtarizadeh, M., Riaz, U., Warren, G., Dizjikan, F. Y., Shorter, T., Straub, V., Bettolo, C. M., Manera, J. D., Hambleton, S., Engelhardt, K., Alexander, E., Peyron, C., Pelissier, A., Beltran, S., Gut, I. G., Laurie, S., Piscia, D., Papakonstantinou, A., Bullich, G., Corvo, A., Fernandez-Callejo, M., Hernandez, C., Pico, D., Lochmuller, H., Gumus, G., Bros-Facer, V., Rath, A., Hanauer, M., Lagorce, D., Hongnat, O., Chahdil, M., Lebreton, E., Stevanin, G., Durr, A., Davoine, C. -S., Guillot-Noel, L., Heinzmann, A., Coarelli, G., Bonne, G., Evangelista, T., Allamand, V., Ben Yaou, R., Metay, C., Eymard, B., Atalaia, A., Stojkovic, T., Turnovec, M., Thomasova, D., Kremlikova, R. P., Frankova, V., Liskova, P., Dolezalova, P., Parkinson, H., Keane, T., Freeberg, M., Thomas, C., Spalding, D., Robert, G., Costa, A., Patch, C., Hanna, M., Houlden, H., Reilly, M., Efthymiou, S., Cali, E., Magrinelli, F., Sisodiya, S. M., Rohrer, J., Muntoni, F., Zaharieva, I., Sarkozy, A., Timmerman, V., Baets, J., de Vries, G., De Winter, J., Beijer, D., de Jonghe, P., Van de Vondel, L., De Ridder, W., Weckhuysen, S., Mutarelli, M., Varavallo, A., Banfi, S., Musacchia, F., Piluso, G., Ferlini, A., Selvatici, R., Gualandi, F., Bigoni, S., Rossi, R., Neri, M., Aretz, S., Spier, I., Sommer, A. K., Peters, S., Oliveira, C., Pelaez, J. G., Matos, A. R., Jose, C. S., Ferreira, M., Gullo, I., Fernandes, S., Garrido, L., Ferreira, P., Carneiro, F., Swertz, M. A., Johansson, L., van der Vries, G., Neerincx, P. B., Ruvolo, D., Kerstjens Frederikse, W. S., Zonneveld-Huijssoon, E., Roelofs-Prins, D., van Gijn, M., Kohler, S., Metcalfe, A., Drunat, S., Heron, D., Mignot, C., Keren, B., Lacombe, D., Capella, G., Valle, L., Holinski-Feder, E., Laner, A., Steinke-Lange, V., Cilio, M. -R., Carpancea, E., Depondt, C., Lederer, D., Sznajer, Y., Duerinckx, S., Mary, S., Macaya, A., Cazurro-Gutierrez, A., Perez-Duenas, B., Munell, F., Jarava, C. F., Maso, L. B., Marce-Grau, A., Colobran, R., Hackman, P., Udd, B., Hemelsoet, D., Dermaut, B., Schuermans, N., Poppe, B., Verdin, H., Osorio, A. N., Depienne, C., Roos, A., Cordts, I., Deschauer, M., Striano, P., Zara, F., Riva, A., Iacomino, M., Uva, P., Scala, M., Scudieri, P., Basak, A. N., Claeys, K., Boztug, K., Haimel, M., W. E, G., Ruivenkamp, C. A. L., Natera de Benito, D., Thompson, R., Polavarapu, K., Grimbacher, B., Zaganas, I., Kokosali, E., Lambros, M., Evangeliou, A., Spilioti, M., Kapaki, E., Bourbouli, M., Balicza, P., Molnar, M. J., De la Paz, M. P., Sanchez, E. B., Delgado, B. M., Alonso Garcia de la Rosa, F. J., Schrock, E., Rump, A., Mei, D., Vetro, A., Balestrini, S., Guerrini, R., Chinnery, P. F., Ratnaike, T., Schon, K., Maver, A., Peterlin, B., Munchau, A., Lohmann, K., Herzog, R., Pauly, M., May, P., Beeson, D., Cossins, J., Furini, S., Afenjar, A., Goldenberg, A., Masurel, A., Phan, A., Dieux-Coeslier, A., Fargeot, A., Guerrot, A. -M., Toutain, A., Molin, A., Sorlin, A., Putoux, A., Jouret, B., Laudier, B., Demeer, B., Doray, B., Bonniaud, B., Isidor, B., Gilbert-Dussardier, B., Leheup, B., Reversade, B., Paul, C., Vincent-Delorme, C., Neiva, C., Poirsier, C., Quelin, C., Chiaverini, C., Coubes, C., Francannet, C., Colson, C., Desplantes, C., Wells, C., Goizet, C., Sanlaville, D., Amram, D., Lehalle, D., Genevieve, D., Gaillard, D., Zivi, E., Sarrazin, E., Steichen, E., Schaefer, E., Lacaze, E., Jacquemin, E., Bongers, E., Kilic, E., Colin, E., Giuliano, F., Prieur, F., Laffargue, F., Morice-Picard, F., Petit, F., Cartault, F., Feillet, F., Baujat, G., Morin, G., Diene, G., Journel, H., Perthus, I., Lespinasse, J., Alessandri, J. -L., Amiel, J., Martinovic, J., Delanne, J., Albuisson, J., Lambert, L., Perrin, L., Ousager, L. B., Van Maldergem, L., Pinson, L., Ruaud, L., Samimi, M., Bournez, M., Bonnet-Dupeyron, M. N., Vincent, M., Jacquemont, M. -L., Cordier-Alex, M. -P., Gerard-Blanluet, M., Willems, M., Spodenkiewicz, M., Doco-Fenzy, M., Rossi, M., Renaud, M., Fradin, M., Mathieu, M., Holder-Espinasse, M. H., Houcinat, N., Hanna, N., Leperrier, N., Chassaing, N., Philip, N., Boute, O., Van Kien, P. K., Parent, P., Bitoun, P., Sarda, P., Vabres, P., Jouk, P. -S., Touraine, R., El Chehadeh, S., Whalen, S., Marlin, S., Passemard, S., Grotto, S., Bellanger, S. A., Blesson, S., Nambot, S., Naudion, S., Lyonnet, S., Odent, S., Attie-Bitach, T., Busa, T., Drouin-Garraud, V., Layet, V., Bizaoui, V., Cusin, V., Capri, Y., Alembik, Y., and Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center]

Subjects
Exome reanalysis, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Multidisciplinaire, généralités & autres [D99] [Sciences de la santé humaine], Developmental disorder, lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], Biology and Life Sciences, Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6], ClinVar, Rare diseases, All institutes and research themes of the Radboud University Medical Center, Medicine and Health Sciences, Genetics & genetic processes [F10] [Life sciences], Génétique & processus génétiques [F10] [Sciences du vivant], Multidisciplinary, general & others [D99] [Human health sciences], Exome reanalysi, Genetics (clinical)
Abstract

Purpose: Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the "ClinVar low-hanging fruit" reanalysis, reasons for the failure of previous analyses, and lessons learned. Methods: Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. Results: We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). Conclusion: The "ClinVar low-hanging fruit" analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock. The Solve-RD project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement number 779257. Data were analyzed using the RD-Connect Genome-Phenome Analysis Platform, which received funding from the EU projects RD-Connect, Solve-RD, and European Joint Programme on Rare Diseases (grant numbers FP7 305444, H2020 779257, H2020 825575), Instituto de Salud Carlos III (grant numbers PT13/0001/0044, PT17/0009/0019; Instituto Nacional de Bioinformática), and ELIXIR Implementation Studies. The collaborations in this study were facilitated by the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies, one of the 24 European Reference Networks approved by the European Reference Network Board of Member States, cofunded by the European Commission. This project was supported by the Czech Ministry of Health (number 00064203) and by the Czech Ministry of Education, Youth and Sports (number - LM2018132) to M.M. Sí

Published
2023

3. Rapid exome sequencing as a first-tier test in neonates with suspected genetic disorder: results of a prospective multicenter clinical utility study in the Netherlands

Author

Olde Keizer, Richelle A.C.M., Marouane, Abderrahim, Kerstjens-Frederikse, Wilhelmina S., Deden, A. Chantal, Lichtenbelt, Klaske D., Jonckers, Tinneke, Vervoorn, Marieke, Vreeburg, M., Henneman, Lidewij, de Vries, Linda S., Sinke, Richard J., Pfundt, Rolph, Stevens, Servi J.C., Andriessen, Peter, van Lingen, Richard A., Nelen, Marcel, Scheffer, Hans, Stemkens, Daphne, Oosterwijk, Cor, van Amstel, Hans Kristian Ploos, de Boode, W. P., van Zelst-Stams, W., Frederix, Geert W.J., Vissers, L. E.L.M., Henneman, L., van Haelst, M. M., Sistermans, E. A., Cornel, M. C., Misra-Isrie, M., Mannens, M. M.A.M., Waisfisz, Q., van Hagen, J. M., Brooks, A. S., Barakat, T. S., Hoefsloot, E. H., van Lingen, R. A., Ruivenkamp, C. A.L., Koene, S., Rutten, J. W., de Koning, B., Stevens, S. J.C., van den Wijngaard, A., Stegmann, A. P.A., Deden, A. C., Rodenburg, W., Sinke, R. J., van der Velde, K. J., de Vries, L. S., Frederix, G. W.J., Oegema, R., Clinical Genetics, Pediatric Surgery, Radiology & Nuclear Medicine, Internal Medicine, Department of Finance, Cell biology, Cardiothoracic Surgery, Molecular Genetics, Pathology, Erasmus School of Law, and Health Economics (HE)

Abstract

The introduction of rapid exome sequencing (rES) for critically ill neonates admitted to the neonatal intensive care unit has made it possible to impact clinical decision-making. Unbiased prospective studies to quantify the impact of rES over routine genetic testing are, however, scarce. We performed a clinical utility study to compare rES to conventional genetic diagnostic workup for critically ill neonates with suspected genetic disorders. In a multicenter prospective parallel cohort study involving five Dutch NICUs, we performed rES in parallel to routine genetic testing for 60 neonates with a suspected genetic disorder and monitored diagnostic yield and the time to diagnosis. To assess the economic impact of rES, healthcare resource use was collected for all neonates. rES detected more conclusive genetic diagnoses than routine genetic testing (20% vs. 10%, respectively), in a significantly shorter time to diagnosis (15 days (95% CI 10–20) vs. 59 days (95% CI 23–98, p < 0.001)). Moreover, rES reduced genetic diagnostic costs by 1.5% (€85 per neonate). Conclusion: Our findings demonstrate the clinical utility of rES for critically ill neonates based on increased diagnostic yield, shorter time to diagnosis, and net healthcare savings. Our observations warrant the widespread implementation of rES as first-tier genetic test in critically ill neonates with disorders of suspected genetic origin.What is Known:• Rapid exome sequencing (rES) enables diagnosing rare genetic disorders in a fast and reliable manner, but retrospective studies with neonates admitted to the neonatal intensive care unit (NICU) indicated that genetic disorders are likely underdiagnosed as rES is not routinely used.• Scenario modeling for implementation of rES for neonates with presumed genetic disorders indicated an expected increase in costs associated with genetic testing.What is New:• This unique prospective national clinical utility study of rES in a NICU setting shows that rES obtained more and faster diagnoses than conventional genetic tests.• Implementation of rES as replacement for all other genetic tests does not increase healthcare costs but in fact leads to a reduction in healthcare costs.

Published
2023

4. A Dutch MYH7 founder mutation, p.(Asn1918Lys), is associated with early onset cardiomyopathy and congenital heart defects

Author

van der Linde, I. H. M., Hiemstra, Y. L., Bökenkamp, R., van Mil, A. M., Breuning, M. H., Ruivenkamp, C., ten Broeke, S. W., Veldkamp, R. F., van Waning, J. I., van Slegtenhorst, M. A., van Spaendonck-Zwarts, K. Y., Lekanne Deprez, R. H., Herkert, J. C., Boven, L., van der Zwaag, P. A., Jongbloed, J. D. H., Bootsma, M., and Barge-Schaapveld, D. Q. C. M.

Published
2017
Full Text
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6. Variants in PHF8 cause a spectrum of X-linked neurodevelopmental disorders and facial dysmorphology

Author

Sobering, A.K., Bryant, L.M., Li, D., McGaughran, J., Maystadt, I., Moortgat, S., Graham, J.M., Haeringen, A. van, Ruivenkamp, C., Cuperus, R., Vogt, J., Morton, J., Brasch-Andersen, C., Steenhof, M., Hansen, L.K., Adler, E., Lyonnet, S., Pingault, V., Sandrine, M., Ziegler, A., Donald, T., Nelson, B., Holt, B., Petryna, O., Firth, H., McWalter, K., Zyskind, J., Telegrafi, A., Juusola, J., Person, R., Bamshad, M.J., Earl, D., Tsai, A.C.H., Yearwood, K.R., Marco, E., Nowak, C., Douglas, J., Hakonarson, H., Bhoj, E.J., and Univ Washington Ctr Mendelian Geno

Subjects
histone demethylation, PHF8, Molecular Medicine, orofacial clefting, Genetics (clinical), epigenetic gene regulation, X-linked intellectual disability
Abstract

Loss-of-function variants in PHD Finger Protein 8 (PHF8) cause Siderius X-linked intellectual disability (ID) syndrome, hereafter called PHF8-XLID. PHF8 is a histone demethylase that is important for epigenetic regulation of gene expression. PHF8-XLID is an under-characterized disorder with only five previous reports describing different PHF8 predicted loss-of-function variants in eight individuals. Features of PHF8-XLID include ID and craniofacial dysmorphology. In this report we present 16 additional individuals with PHF8-XLID from 11 different families of diverse ancestry. We also present five individuals from four different families who have ID and a variant of unknown significance in PHF8 with no other explanatory variant in another gene. All affected individuals exhibited developmental delay and all but two had borderline to severe ID. Of the two who did not have ID, one had dyscalculia and the other had mild learning difficulties. Craniofacial findings such as hypertelorism, microcephaly, elongated face, ptosis, and mild facial asymmetry were found in some affected individuals. Orofacial clefting was seen in three individuals from our cohort, suggesting that this feature is less common than previously reported. Autism spectrum disorder and attention deficit hyperactivity disorder, which were not previously emphasized in PHF8-XLID, were frequently observed in affected individuals. This series expands the clinical phenotype of this rare ID syndrome caused by loss of PHF8 function.

Published
2022

7. PURA-Related Developmental and Epileptic Encephalopathy

Author

Johannesen, K.M., Gardella, E., Gjerulfsen, C.E., Bayat, A., Rouhl, R.P.W., Reijnders, M., Whalen, S., Keren, B., Buratti, J., Courtin, T., Wierenga, K.J., Isidor, B., Piton, A., Faivre, L., Garde, A., Moutton, S., Tran-Mau-Them, F., Denomme-Pichon, A.S., Coubes, C., Larson, A., Esser, M.J., Appendino, J.P., Al-Hertani, W., Gamboni, B., Mampel, A., Mayorga, L., Orsini, A., Bonuccelli, A., Suppiej, A., Van-Gils, J., Vogt, J., Damioli, S., Giordano, L., Moortgat, S., Wirrell, E., Hicks, S., Kini, U., Noble, N., Stewart, H., Asakar, S., Cohen, J.S., Naidu, S.R., Collier, A., Brilstra, E.H., Li, M.H., Brew, C., Bigoni, S., Ognibene, D., Ballardini, E., Ruivenkamp, C., RS: MHeNs - R1 - Cognitive Neuropsychiatry and Clinical Neuroscience, Klinische Neurowetenschappen, MUMC+: MA Med Staf Spec Neurologie (9), and MUMC+: DA KG Polikliniek (9)

Subjects
ALPHA, DELINEATION, EPILEPSIES, DE-NOVO MUTATIONS, MORTALITY, FEATURES, PHENOTYPE, CLASSIFICATION, POSTNATAL BRAIN-DEVELOPMENT
Abstract

Background and ObjectivesPurine-rich element-binding protein A (PURA) gene encodes Pur-alpha, a conserved protein essential for normal postnatal brain development. Recently, a PURA syndrome characterized by intellectual disability, hypotonia, epilepsy, and dysmorphic features was suggested. The aim of this study was to define and expand the phenotypic spectrum of PURA syndrome by collecting data, including EEG, from a large cohort of affected patients.MethodsData on unpublished and published cases were collected through the PURA Syndrome Foundation and the literature. Data on clinical, genetic, neuroimaging, and neurophysiologic features were obtained.ResultsA cohort of 142 patients was included. Characteristics of the PURA syndrome included neonatal hypotonia, feeding difficulties, and respiratory distress. Sixty percent of the patients developed epilepsy with myoclonic, generalized tonic-clonic, focal seizures, and/or epileptic spasms. EEG showed generalized, multifocal, or focal epileptic abnormalities. Lennox-Gastaut was the most common epilepsy syndrome. Drug refractoriness was common: 33.3% achieved seizure freedom. We found 97 pathogenic variants in PURA without any clear genotype-phenotype associations.DiscussionThe PURA syndrome presents with a developmental and epileptic encephalopathy with characteristics recognizable from neonatal age, which should prompt genetic screening. Sixty percent have drug-resistant epilepsy with focal or generalized seizures. We collected more than 90 pathogenic variants without observing overt genotype-phenotype associations.

Published
2021

9. Truncating SRCAP variants outside the Floating-Harbor syndrome locus cause a distinct neurodevelopmental disorder with a specific DNA methylation signature

Author

Rots, D., Chater-Diehl, E., Dingemans, A.J.M., Goodman, S.J., Siu, M.T., Cytrynbaum, C., Choufani, S., Hoang, N., Walker, S., Awamleh, Z., Charkow, J., Meyn, S., Pfundt, R.P., Rinne, T.K., Gardeitchik, T., Vries, B.B.A. de, Deden, A.C., Leenders, E.K.S.M., Kwint, M.P., Stumpel, C., Stevens, S.J.C., Vermeulen, J.R., Harssel, J.V.T. van, Bosch, D.G.M., Gassen, K.L.I. van, Binsbergen, E. van, Geus, C.M. de, Brackel, H., Hempel, M., Lessel, D., Denecke, J., Slavotinek, A., Strober, J., Crunk, A., Folk, L., Wentzensen, I.M., Yang, H., Zou, F., Millan, F., Person, R., Xie, Y., Liu, S., Ousager, L.B., Larsen, M., Schultz-Rogers, L., Morava, E., Klee, E.W., Berry, I.R., Campbell, J., Lindstrom, K., Pruniski, B., Neumeyer, A.M., Radley, J.A., Phornphutkul, C., Schmidt, B., Wilson, W.G., Õunap, K., Reinson, K., Pajusalu, S., Haeringen, A. van, Ruivenkamp, C., Cuperus, R., Santos-Simarro, F., Palomares-Bralo, M., Pacio-Míguez, M., Ritter, A., Bhoj, E., Tønne, E., Tveten, K., Cappuccio, G., Brunetti-Pierri, N., Rowe, L., Bunn, J., Saenz, M., Platzer, K., Mertens, M., Caluseriu, O., Nowaczyk, M.J., Cohn, R.D., Kannu, P., Alkhunaizi, E., Chitayat, D., Scherer, S.W., Brunner, H.G., Vissers, L.E., Kleefstra, T., Koolen, D.A., Weksberg, R., Rots, D., Chater-Diehl, E., Dingemans, A.J.M., Goodman, S.J., Siu, M.T., Cytrynbaum, C., Choufani, S., Hoang, N., Walker, S., Awamleh, Z., Charkow, J., Meyn, S., Pfundt, R.P., Rinne, T.K., Gardeitchik, T., Vries, B.B.A. de, Deden, A.C., Leenders, E.K.S.M., Kwint, M.P., Stumpel, C., Stevens, S.J.C., Vermeulen, J.R., Harssel, J.V.T. van, Bosch, D.G.M., Gassen, K.L.I. van, Binsbergen, E. van, Geus, C.M. de, Brackel, H., Hempel, M., Lessel, D., Denecke, J., Slavotinek, A., Strober, J., Crunk, A., Folk, L., Wentzensen, I.M., Yang, H., Zou, F., Millan, F., Person, R., Xie, Y., Liu, S., Ousager, L.B., Larsen, M., Schultz-Rogers, L., Morava, E., Klee, E.W., Berry, I.R., Campbell, J., Lindstrom, K., Pruniski, B., Neumeyer, A.M., Radley, J.A., Phornphutkul, C., Schmidt, B., Wilson, W.G., Õunap, K., Reinson, K., Pajusalu, S., Haeringen, A. van, Ruivenkamp, C., Cuperus, R., Santos-Simarro, F., Palomares-Bralo, M., Pacio-Míguez, M., Ritter, A., Bhoj, E., Tønne, E., Tveten, K., Cappuccio, G., Brunetti-Pierri, N., Rowe, L., Bunn, J., Saenz, M., Platzer, K., Mertens, M., Caluseriu, O., Nowaczyk, M.J., Cohn, R.D., Kannu, P., Alkhunaizi, E., Chitayat, D., Scherer, S.W., Brunner, H.G., Vissers, L.E., Kleefstra, T., Koolen, D.A., and Weksberg, R.

Abstract

Contains fulltext : 234078.pdf (Publisher’s version ) (Open Access), Truncating variants in exons 33 and 34 of the SNF2-related CREBBP activator protein (SRCAP) gene cause the neurodevelopmental disorder (NDD) Floating-Harbor syndrome (FLHS), characterized by short stature, speech delay, and facial dysmorphism. Here, we present a cohort of 33 individuals with clinical features distinct from FLHS and truncating (mostly de novo) SRCAP variants either proximal (n = 28) or distal (n = 5) to the FLHS locus. Detailed clinical characterization of the proximal SRCAP individuals identified shared characteristics: developmental delay with or without intellectual disability, behavioral and psychiatric problems, non-specific facial features, musculoskeletal issues, and hypotonia. Because FLHS is known to be associated with a unique set of DNA methylation (DNAm) changes in blood, a DNAm signature, we investigated whether there was a distinct signature associated with our affected individuals. A machine-learning model, based on the FLHS DNAm signature, negatively classified all our tested subjects. Comparing proximal variants with typically developing controls, we identified a DNAm signature distinct from the FLHS signature. Based on the DNAm and clinical data, we refer to the condition as "non-FLHS SRCAP-related NDD." All five distal variants classified negatively using the FLHS DNAm model while two classified positively using the proximal model. This suggests divergent pathogenicity of these variants, though clinically the distal group presented with NDD, similar to the proximal SRCAP group. In summary, for SRCAP, there is a clear relationship between variant location, DNAm profile, and clinical phenotype. These results highlight the power of combined epigenetic, molecular, and clinical studies to identify and characterize genotype-epigenotype-phenotype correlations.

Published
2021

10. CSNK2B: A broad spectrum of neurodevelopmental disability and epilepsy severity

Author

Ernst, ME, Baugh, EH, Thomas, A, Bier, L, Lippa, N, Stong, N, Mulhern, MS, Kushary, S, Akman, CI, Heinzen, EL, Yeh, R, Bi, W, Hanchard, NA, Burrage, LC, Leduc, MS, Chong, JSC, Bend, R, Lyons, MJ, Lee, JA, Suwannarat, P, Brilstra, E, Simon, M, Koopmans, M, van Binsbergen, E, Groepper, D, Fleischer, J, Nava, C, Keren, B, Mignot, C, Mathieu, S, Mancini, GMS, Madan-Khetarpal, S, Infante, EM, Bluvstein, J, Seeley, A, Bachman, K, Klee, EW, Schultz-Rogers, LE, Hasadsri, L, Barnett, S, Ellingson, MS, Ferber, MJ, Narayanan, V, Ramsey, K, Rauch, A, Joset, P, Steindl, K, Sheehan, T, Poduri, A, Vasquez, A, Ruivenkamp, C, White, SM, Pais, L, Monaghan, KG, Goldstein, DB, Sands, TT, Aggarwal, V, Ernst, ME, Baugh, EH, Thomas, A, Bier, L, Lippa, N, Stong, N, Mulhern, MS, Kushary, S, Akman, CI, Heinzen, EL, Yeh, R, Bi, W, Hanchard, NA, Burrage, LC, Leduc, MS, Chong, JSC, Bend, R, Lyons, MJ, Lee, JA, Suwannarat, P, Brilstra, E, Simon, M, Koopmans, M, van Binsbergen, E, Groepper, D, Fleischer, J, Nava, C, Keren, B, Mignot, C, Mathieu, S, Mancini, GMS, Madan-Khetarpal, S, Infante, EM, Bluvstein, J, Seeley, A, Bachman, K, Klee, EW, Schultz-Rogers, LE, Hasadsri, L, Barnett, S, Ellingson, MS, Ferber, MJ, Narayanan, V, Ramsey, K, Rauch, A, Joset, P, Steindl, K, Sheehan, T, Poduri, A, Vasquez, A, Ruivenkamp, C, White, SM, Pais, L, Monaghan, KG, Goldstein, DB, Sands, TT, and Aggarwal, V

Abstract

CSNK2B has recently been implicated as a disease gene for neurodevelopmental disability (NDD) and epilepsy. Information about developmental outcomes has been limited by the young age and short follow-up for many of the previously reported cases, and further delineation of the spectrum of associated phenotypes is needed. We present 25 new patients with variants in CSNK2B and refine the associated NDD and epilepsy phenotypes. CSNK2B variants were identified by research or clinical exome sequencing, and investigators from different centers were connected via GeneMatcher. Most individuals had developmental delay and generalized epilepsy with onset in the first 2 years. However, we found a broad spectrum of phenotypic severity, ranging from early normal development with pharmacoresponsive seizures to profound intellectual disability with intractable epilepsy and recurrent refractory status epilepticus. These findings suggest that CSNK2B should be considered in the diagnostic evaluation of patients with a broad range of NDD with treatable or intractable seizures.

Published
2021

11. Location, location, location: protein truncating variants in different loci of SRCAP cause three distinct neurodevelopmental disorders, associated with distinctive DNA methylation signatures

Author

Rots, D., Chater-Diehl, E., Dingemans, A. J. M., Siu, M., Cytrynbaum, C., Hoang, N., Walker, S., Scherer, S., Pfundt, R., Rinne, T., Gardeitchik, T., Vries, B. B. A., Stumpel, C. T. R. M., Stevens, S. J. C., Harssel, J., Bosch, D. G. M., Gassen, K. L. I., Binsbergen, E., Geus, C. M., Hempel, M., Lessel, D., Denecke, J., Slavotinek, A., Strober, J., Lilian Bomme Ousager, Martin Jakob Larsen, Schultz-Rogers, L., Morava, E., Klee, E. W., Berry, I. R., Campbell, J., Lindstrom, K., Neumeyer, A. M., Radley, J. A., Phornphutkul, C., Wilson, W. G., Schmidt, B., Meyn, S., Ounap, K., Reinson, K., Pajusalu, S., Ruivenkamp, C., Haeringen, A., Cuperus, R., Vissers, L. E. L. M., Brunner, H. G., Kleefstra, T., Koolen, D. A., Weksberg, R., and GeneDx Inc

Published
2020

12. Phenotypic and genotypic description of 44 patients with variants in DLG4 encoding the post-synaptic density protein PSD-95

Author

Rodriguez-Palmero Seuma, A., Boerrigter, M., Mandrile, G., Pelle, A., Giorgio, E., Lindstrand, A., Johansson, M., Kvarnung, M., Everman, D., Bahrambeigi, V., MacKenzie, A., Morton, J., Ruivenkamp, C., Challman, T., Hurst, A., Hoyer, J., Elmslie, F., Dye, T., Isidor, B., Haldeman-Englert, C., Gomez-Andres, D., Schluter, A., de Man, S., Shieh, J., Prada, C., Moutton, S., Denomme-Pichon, A., Motti, S., Bruel, A., Mau-Them, F. Tran, Reiter, S., van Ravenswaaij-Arts, C., Shaw-Smith, C., Parikh, S., Aldinger, K., Lovgren, A., Rauch, A., Ross, M., Gomez-Puertas, P., de Vries, B., Pujol, A., Tumer, Z., and Clinical Cognitive Neuropsychiatry Research Program (CCNP)

Published
2020

13. De Novo Variants in CNOT1, a Central Component of the CCR4-NOT Complex Involved in Gene Expression and RNA and Protein Stability, Cause Neurodevelopmental Delay

Author

Vissers, L.E.L.M., Kalvakuri, S., Boer, E. de, Geuer, S., Oud, M.M., Outersterp, I. van, Kwint, M.P., Witmond, M., Kersten, S., Polla, D.L., Weijers, D., Begtrup, A., McWalter, K., Ruiz, A., Gabau, E., Morton, J.E., Griffith, C., Weiss, K., Gamble, C., Bartley, J., Vernon, H.J., Brunet, K., Ruivenkamp, C., Kant, S.G., Kruszka, P., Larson, A., Afenjar, A., Billette de Villemeur, T., Nugent, K., Raymond, F.L., Venselaar, H., Demurger, F., Soler-Alfonso, C., Li, D., Bhoj, E., Hayes, I., Hamilton, N.P., Ahmad, A., Fisher, R., Born, M. van den, Willems, M., Sorlin, A., Delanne, J., Moutton, S., Christophe, P., Mau-Them, F.T., Vitobello, A., Goel, H., Massingham, L., Phornphutkul, C., Schwab, J., Keren, B., Charles, P., Vreeburg, M., Simone, L. De, Hoganson, G., Iascone, M., Milani, D., Evenepoel, L., Revencu, N., Ward, D.I., Burns, K., Krantz, I., Raible, S.E., Murrell, J.R., Wood, K., Cho, M.T., Bokhoven, H. van, Muenke, M., Kleefstra, T., Bodmer, R., Brouwer, A.P.M. de, Vissers, L.E.L.M., Kalvakuri, S., Boer, E. de, Geuer, S., Oud, M.M., Outersterp, I. van, Kwint, M.P., Witmond, M., Kersten, S., Polla, D.L., Weijers, D., Begtrup, A., McWalter, K., Ruiz, A., Gabau, E., Morton, J.E., Griffith, C., Weiss, K., Gamble, C., Bartley, J., Vernon, H.J., Brunet, K., Ruivenkamp, C., Kant, S.G., Kruszka, P., Larson, A., Afenjar, A., Billette de Villemeur, T., Nugent, K., Raymond, F.L., Venselaar, H., Demurger, F., Soler-Alfonso, C., Li, D., Bhoj, E., Hayes, I., Hamilton, N.P., Ahmad, A., Fisher, R., Born, M. van den, Willems, M., Sorlin, A., Delanne, J., Moutton, S., Christophe, P., Mau-Them, F.T., Vitobello, A., Goel, H., Massingham, L., Phornphutkul, C., Schwab, J., Keren, B., Charles, P., Vreeburg, M., Simone, L. De, Hoganson, G., Iascone, M., Milani, D., Evenepoel, L., Revencu, N., Ward, D.I., Burns, K., Krantz, I., Raible, S.E., Murrell, J.R., Wood, K., Cho, M.T., Bokhoven, H. van, Muenke, M., Kleefstra, T., Bodmer, R., and Brouwer, A.P.M. de

Abstract

Contains fulltext : 220423.pdf (Publisher’s version ) (Closed access), CNOT1 is a member of the CCR4-NOT complex, which is a master regulator, orchestrating gene expression, RNA deadenylation, and protein ubiquitination. We report on 39 individuals with heterozygous de novo CNOT1 variants, including missense, splice site, and nonsense variants, who present with a clinical spectrum of intellectual disability, motor delay, speech delay, seizures, hypotonia, and behavioral problems. To link CNOT1 dysfunction to the neurodevelopmental phenotype observed, we generated variant-specific Drosophila models, which showed learning and memory defects upon CNOT1 knockdown. Introduction of human wild-type CNOT1 was able to rescue this phenotype, whereas mutants could not or only partially, supporting our hypothesis that CNOT1 impairment results in neurodevelopmental delay. Furthermore, the genetic interaction with autism-spectrum genes, such as ASH1L, DYRK1A, MED13, and SHANK3, was impaired in our Drosophila models. Molecular characterization of CNOT1 variants revealed normal CNOT1 expression levels, with both mutant and wild-type alleles expressed at similar levels. Analysis of protein-protein interactions with other members indicated that the CCR4-NOT complex remained intact. An integrated omics approach of patient-derived genomics and transcriptomics data suggested only minimal effects on endonucleolytic nonsense-mediated mRNA decay components, suggesting that de novo CNOT1 variants are likely haploinsufficient hypomorph or neomorph, rather than dominant negative. In summary, we provide strong evidence that de novo CNOT1 variants cause neurodevelopmental delay with a wide range of additional co-morbidities. Whereas the underlying pathophysiological mechanism warrants further analysis, our data demonstrate an essential and central role of the CCR4-NOT complex in human brain development.

Published
2020

15. Thrombocytopenia with Absent Radii (TAR) syndrome is cause by compound inheritance of low-frequency regulatory SNPs and a rare null mutation in exon-junction complex subunit RBM8A: 18

Author

Albers, C A, Paul, D S, Schulze, H, Freson, K, Stephens, J C, Smethurst, P A, Jolley, J D, Cvejic, A, Kostadima, M, Bertone, P, Breuning, M H, Debili, N, Deloukas, P, Favier, R, Fiedler, J, Hobbs, C M, Huang, N, Hurles, M E, Kiddle, G, Krapels, I, Nurden, P, Ruivenkamp, C AL, Sambrook, J G, Smith, K, Stemple, D L, Strauss, G, Thys, C, van Geet, C, Newbury-Ecob, R, Ouwehand, W H, and Ghevaert, C

Published
2012

21. Mutations in the Chromatin Regulator Gene BRPF1 Cause Syndromic Intellectual Disability and Deficient Histone Acetylation

Author

Yan, K.Z., Rousseau, J., Littlejohn, R.O., Kiss, C., Lehman, A., Rosenfeld, J.A., Stumpel, C.T.R., Stegmann, A.P.A., Robak, L., Scaglia, F., Nguyen, T.T.M., Fu, H., Ajeawung, N.F., Camurri, M.V., Li, L., Gardham, A., Panis, B., Almannai, M., Sacoto, M.J.G., Baskin, B., Ruivenkamp, C., Xia, F., Bi, W., Cho, M.T., Potjer, T.P., Santen, G.W.E., Parker, M.J., Canham, N., McKinnon, M., Potocki, L., MacKenzie, J.J., Roeder, E.R., Campeau, P.M., Yang, X.J., DDD Study, CAUSES Study, MUMC+: DA KG Polikliniek (9), RS: GROW - R4 - Reproductive and Perinatal Medicine, Klinische Genetica, and MUMC+: DA KG Lab Centraal Lab (9)

Subjects
0301 basic medicine, Male, Developmental Disabilities, PZP DOMAIN, HBO1 ACETYLTRANSFERASE, Histones, Mice, Intellectual disability, Global developmental delay, Child, Genetics (clinical), Histone Acetyltransferases, Genetics, Mice, Knockout, ZINC-FINGER PROTEIN, Nuclear Proteins, Acetylation, Syndrome, Chromatin, DNA-Binding Proteins, Histone, Muscle Hypotonia, Female, EXPRESSION, Adolescent, Biology, KAT6B, Article, 03 medical and health sciences, Histone H3, Intellectual Disability, medicine, Animals, Humans, HEMATOPOIETIC STEM-CELLS, Epigenetics, Histone H3 acetylation, Alleles, Adaptor Proteins, Signal Transducing, CAUSE GENITOPATELLAR SYNDROME, Lysine, PHD FINGER, medicine.disease, Bromodomain, Mice, Inbred C57BL, 030104 developmental biology, DE-NOVO MUTATIONS, Face, Mutation, biology.protein, Carrier Proteins, CAENORHABDITIS-ELEGANS
Abstract

Identification of over 500 epigenetic regulators in humans raises an interesting question regarding how chromatin dysregulation contributes to different diseases. Bromodomain and PHD finger-containing protein 1 (BRPF1) is a multivalent chromatin regulator possessing three histone-binding domains, one non-specific DNA-binding module, and several motifs for interacting with and activating three lysine acetyltransferases. Genetic analyses of fish brpf1 and mouse Brpf1 have uncovered an important role in skeletal, hematopoietic, and brain development, but it remains unclear how BRPF1 is linked to human development and disease. Here, we describe an intellectual disability disorder in ten individuals with inherited or de novo monoallelic BRPF1 mutations. Syrhptoms include infantile hypotonia, global developmental delay, intellectual disability, expressive language impairment, and facial dysmorphisms. Central nervous system and spinal abnormalities are also seen in some individuals. These clinical features overlap with but are not identical to those reported for persons with KAT6A or KAT6B mutations, suggesting that BRPF1 targets these two acetyltransferases and additional partners in humans. Functional assays showed that the resulting BRPF1 variants are pathogenic and impair acetylation of histone H3 at lysine 23, an abundant but poorly characterized epigenetic mark. We also found a similar deficiency in different lines of Brpf1-knockout mice. These data indicate that aberrations in the chromatin regulator gene BRPF1 cause histone H3 acetylation deficiency and a previously unrecognized intellectual disability syndrome.

Published
2017

23. A recurrent de novo PACS2 heterozygous missense variant causes neonatal-onset developmental epileptic encephalopathy, facial dysmorphism and cerebellar dysgenesis

Author

Jean-Marcais, N., Olson, H. E., Yang, E., Heron, D., Tatton-Brown, K., van der Zwaag, P. A., Bijlsma, E. K., Krock, B. L., Backer, E., Kamsteeg, E., Sinnema, M., Reijnders, M. R. F., Bearden, D., Lunsing, R. J., Burglen, L., Lesca, G., Smith, L. A., Sheidley, B., Pearl, P. L., El Achkar, C. Moufawad, Poduri, A., Skraban, C. M., Nesbitt, A. I., van de Putte, D. E. Fransen, Ruivenkamp, C. A. L., Rump, P., Sabatier, I., Sweetser, D. A., Waxler, J. L., Tarpinian, J., Wierenga, K. J., Donadieu, J., Narayanan, V., Ramsey, K. M., Nava, C., Lelieveld, S. H., Schuurs-Hoeijmakers, J., Brunner, H. G., Keren, B., Mau-Them, F. Tran, Thevenon, J., Faivre, L., Thomas, G., and Thauvin-Robinet, C.

Published
2019

24. AMPA receptor GluA2 subunit defects are a cause of neurodevelopmental disorders

Author

Salpietro, V. Dixon, C.L. Guo, H. Bello, O.D. Vandrovcova, J. Efthymiou, S. Maroofian, R. Heimer, G. Burglen, L. Valence, S. Torti, E. Hacke, M. Rankin, J. Tariq, H. Colin, E. Procaccio, V. Striano, P. Mankad, K. Lieb, A. Chen, S. Pisani, L. Bettencourt, C. Männikkö, R. Manole, A. Brusco, A. Grosso, E. Ferrero, G.B. Armstrong-Moron, J. Gueden, S. Bar-Yosef, O. Tzadok, M. Monaghan, K.G. Santiago-Sim, T. Person, R.E. Cho, M.T. Willaert, R. Yoo, Y. Chae, J.-H. Quan, Y. Wu, H. Wang, T. Bernier, R.A. Xia, K. Blesson, A. Jain, M. Motazacker, M.M. Jaeger, B. Schneider, A.L. Boysen, K. Muir, A.M. Myers, C.T. Gavrilova, R.H. Gunderson, L. Schultz-Rogers, L. Klee, E.W. Dyment, D. Osmond, M. Parellada, M. Llorente, C. Gonzalez-Peñas, J. Carracedo, A. Van Haeringen, A. Ruivenkamp, C. Nava, C. Heron, D. Nardello, R. Iacomino, M. Minetti, C. Skabar, A. Fabretto, A. Hanna, M.G. Bugiardini, E. Hostettler, I. O’Callaghan, B. Khan, A. Cortese, A. O’Connor, E. Yau, W.Y. Bourinaris, T. Kaiyrzhanov, R. Chelban, V. Madej, M. Diana, M.C. Vari, M.S. Pedemonte, M. Bruno, C. Balagura, G. Scala, M. Fiorillo, C. Nobili, L. Malintan, N.T. Zanetti, M.N. Krishnakumar, S.S. Lignani, G. Jepson, J.E.C. Broda, P. Baldassari, S. Rossi, P. Fruscione, F. Madia, F. Traverso, M. De-Marco, P. Pérez-Dueñas, B. Munell, F. Kriouile, Y. El-Khorassani, M. Karashova, B. Avdjieva, D. Kathom, H. Tincheva, R. Van-Maldergem, L. Nachbauer, W. Boesch, S. Gagliano, A. Amadori, E. Goraya, J.S. Sultan, T. Kirmani, S. Ibrahim, S. Jan, F. Mine, J. Banu, S. Veggiotti, P. Zuccotti, G.V. Ferrari, M.D. Van Den Maagdenberg, A.M.J. Verrotti, A. Marseglia, G.L. Savasta, S. Soler, M.A. Scuderi, C. Borgione, E. Chimenz, R. Gitto, E. Dipasquale, V. Sallemi, A. Fusco, M. Cuppari, C. Cutrupi, M.C. Ruggieri, M. Cama, A. Capra, V. Mencacci, N.E. Boles, R. Gupta, N. Kabra, M. Papacostas, S. Zamba-Papanicolaou, E. Dardiotis, E. Maqbool, S. Rana, N. Atawneh, O. Lim, S.Y. Shaikh, F. Koutsis, G. Breza, M. Coviello, D.A. Dauvilliers, Y.A. AlKhawaja, I. AlKhawaja, M. Al-Mutairi, F. Stojkovic, T. Ferrucci, V. Zollo, M. Alkuraya, F.S. Kinali, M. Sherifa, H. Benrhouma, H. Turki, I.B.Y. Tazir, M. Obeid, M. Bakhtadze, S. Saadi, N.W. Zaki, M.S. Triki, C.C. Benfenati, F. Gustincich, S. Kara, M. Belcastro, V. Specchio, N. Capovilla, G. Karimiani, E.G. Salih, A.M. Okubadejo, N.U. Ojo, O.O. Oshinaike, O.O. Oguntunde, O. Wahab, K. Bello, A.H. Abubakar, S. Obiabo, Y. Nwazor, E. Ekenze, O. Williams, U. Iyagba, A. Taiwo, L. Komolafe, M. Senkevich, K. Shashkin, C. Zharkynbekova, N. Koneyev, K. Manizha, G. Isrofilov, M. Guliyeva, U. Salayev, K. Khachatryan, S. Rossi, S. Silvestri, G. Haridy, N. Ramenghi, L.A. Xiromerisiou, G. David, E. Aguennouz, M. Fidani, L. Spanaki, C. Tucci, A. Raspall-Chaure, M. Chez, M. Tsai, A. Fassi, E. Shinawi, M. Constantino, J.N. De Zorzi, R. Fortuna, S. Kok, F. Keren, B. Bonneau, D. Choi, M. Benzeev, B. Zara, F. Mefford, H.C. Scheffer, I.E. Clayton-Smith, J. Macaya, A. Rothman, J.E. Eichler, E.E. Kullmann, D.M. Houlden, H. SYNAPS Study Group

Abstract

AMPA receptors (AMPARs) are tetrameric ligand-gated channels made up of combinations of GluA1-4 subunits encoded by GRIA1-4 genes. GluA2 has an especially important role because, following post-transcriptional editing at the Q607 site, it renders heteromultimeric AMPARs Ca2+-impermeable, with a linear relationship between current and trans-membrane voltage. Here, we report heterozygous de novo GRIA2 mutations in 28 unrelated patients with intellectual disability (ID) and neurodevelopmental abnormalities including autism spectrum disorder (ASD), Rett syndrome-like features, and seizures or developmental epileptic encephalopathy (DEE). In functional expression studies, mutations lead to a decrease in agonist-evoked current mediated by mutant subunits compared to wild-type channels. When GluA2 subunits are co-expressed with GluA1, most GRIA2 mutations cause a decreased current amplitude and some also affect voltage rectification. Our results show that de-novo variants in GRIA2 can cause neurodevelopmental disorders, complementing evidence that other genetic causes of ID, ASD and DEE also disrupt glutamatergic synaptic transmission. © 2019, The Author(s).

Published
2019

26. AMPA receptor GluA2 subunit defects are a cause of neurodevelopmental disorders

Author

Salpietro, V, Dixon, CL, Guo, H, Bello, OD, Vandrovcova, J, Efthymiou, S, Maroofian, R, Heimer, G, Burglen, L, Valence, S, Torti, E, Hacke, M, Rankin, J, Tariq, H, Colin, E, Procaccio, V, Striano, P, Mankad, K, Lieb, A, Chen, S, Pisani, L, Bettencourt, C, Mannikko, R, Manole, A, Brusco, A, Grosso, E, Ferrero, GB, Armstrong-Moron, J, Gueden, S, Bar-Yosef, O, Tzadok, M, Monaghan, KG, Santiago-Sim, T, Person, RE, Cho, MT, Willaert, R, Yoo, Y, Chae, J-H, Quan, Y, Wu, H, Wang, T, Bernier, RA, Xia, K, Blesson, A, Jain, M, Motazacker, MM, Jaeger, B, Schneider, AL, Boysen, K, Muir, AM, Myers, CT, Gavrilova, RH, Gunderson, L, Schultz-Rogers, L, Klee, EW, Dyment, D, Osmond, M, Parellada, M, Llorente, C, Gonzalez-Penas, J, Carracedo, A, Van Haeringen, A, Ruivenkamp, C, Nava, C, Heron, D, Nardello, R, Iacomino, M, Minetti, C, Skabar, A, Fabretto, A, Chez, M, Tsai, A, Fassi, E, Shinawi, M, Constantino, JN, De Zorzi, R, Fortuna, S, Kok, F, Keren, B, Bonneau, D, Choi, M, Benzeev, B, Zara, F, Mefford, HC, Scheffer, IE, Clayton-Smith, J, Macaya, A, Rothman, JE, Eichler, EE, Kullmann, DM, Houlden, H, Raspall-Chaure, M, Hanna, MG, Bugiardini, E, Hostettler, I, O'Callaghan, B, Khan, A, Cortese, A, O'Connor, E, Yau, WY, Bourinaris, T, Kaiyrzhanov, R, Chelban, V, Madej, M, Diana, MC, Vari, MS, Pedemonte, M, Bruno, C, Balagura, G, Scala, M, Fiorillo, C, Nobili, L, Malintan, NT, Zanetti, MN, Krishnakumar, SS, Lignani, G, Jepson, JEC, Broda, P, Baldassari, S, Rossi, P, Fruscione, F, Madia, F, Traverso, M, De-Marco, P, Perez-Duenas, B, Munell, F, Kriouile, Y, El-Khorassani, M, Karashova, B, Avdjieva, D, Kathom, H, Tincheva, R, Van-Maldergem, L, Nachbauer, W, Boesch, S, Gagliano, A, Amadori, E, Goraya, JS, Sultan, T, Kirmani, S, Ibrahim, S, Jan, F, Mine, J, Banu, S, Veggiotti, P, Zuccotti, G, Ferrari, MD, Van Den Maagdenberg, AMJ, Verrotti, A, Marseglia, GL, Savasta, S, Soler, MA, Scuderi, C, Borgione, E, Chimenz, R, Gitto, E, Dipasquale, V, Sallemi, A, Fusco, M, Cuppari, C, Cutrupi, MC, Ruggieri, M, Cama, A, Capra, V, Mencacci, NE, Boles, R, Gupta, N, Kabra, M, Papacostas, S, Zamba-Papanicolaou, E, Dardiotis, E, Maqbool, S, Rana, N, Atawneh, O, Lim, SY, Shaikh, F, Koutsis, G, Breza, M, Coviello, DA, Dauvilliers, YA, AlKhawaja, I, AlKhawaja, M, Al-Mutairi, F, Stojkovic, T, Ferrucci, V, Zollo, M, Alkuraya, FS, Kinali, M, Sherifa, H, Benrhouma, H, Turki, IBY, Tazir, M, Obeid, M, Bakhtadze, S, Saadi, NW, Zaki, MS, Triki, CC, Benfenati, F, Gustincich, S, Kara, M, Belcastro, V, Specchio, N, Capovilla, G, Karimiani, EG, Salih, AM, Okubadejo, NU, Ojo, OO, Oshinaike, OO, Oguntunde, O, Wahab, K, Bello, AH, Abubakar, S, Obiabo, Y, Nwazor, E, Ekenze, O, Williams, U, Iyagba, A, Taiwo, L, Komolafe, M, Senkevich, K, Shashkin, C, Zharkynbekova, N, Koneyev, K, Manizha, G, Isrofilov, M, Guliyeva, U, Salayev, K, Khachatryan, S, Rossi, S, Silvestri, G, Haridy, N, Ramenghi, LA, Xiromerisiou, G, David, E, Aguennouz, M, Fidani, L, Spanaki, C, Tucci, A, Salpietro, V, Dixon, CL, Guo, H, Bello, OD, Vandrovcova, J, Efthymiou, S, Maroofian, R, Heimer, G, Burglen, L, Valence, S, Torti, E, Hacke, M, Rankin, J, Tariq, H, Colin, E, Procaccio, V, Striano, P, Mankad, K, Lieb, A, Chen, S, Pisani, L, Bettencourt, C, Mannikko, R, Manole, A, Brusco, A, Grosso, E, Ferrero, GB, Armstrong-Moron, J, Gueden, S, Bar-Yosef, O, Tzadok, M, Monaghan, KG, Santiago-Sim, T, Person, RE, Cho, MT, Willaert, R, Yoo, Y, Chae, J-H, Quan, Y, Wu, H, Wang, T, Bernier, RA, Xia, K, Blesson, A, Jain, M, Motazacker, MM, Jaeger, B, Schneider, AL, Boysen, K, Muir, AM, Myers, CT, Gavrilova, RH, Gunderson, L, Schultz-Rogers, L, Klee, EW, Dyment, D, Osmond, M, Parellada, M, Llorente, C, Gonzalez-Penas, J, Carracedo, A, Van Haeringen, A, Ruivenkamp, C, Nava, C, Heron, D, Nardello, R, Iacomino, M, Minetti, C, Skabar, A, Fabretto, A, Chez, M, Tsai, A, Fassi, E, Shinawi, M, Constantino, JN, De Zorzi, R, Fortuna, S, Kok, F, Keren, B, Bonneau, D, Choi, M, Benzeev, B, Zara, F, Mefford, HC, Scheffer, IE, Clayton-Smith, J, Macaya, A, Rothman, JE, Eichler, EE, Kullmann, DM, Houlden, H, Raspall-Chaure, M, Hanna, MG, Bugiardini, E, Hostettler, I, O'Callaghan, B, Khan, A, Cortese, A, O'Connor, E, Yau, WY, Bourinaris, T, Kaiyrzhanov, R, Chelban, V, Madej, M, Diana, MC, Vari, MS, Pedemonte, M, Bruno, C, Balagura, G, Scala, M, Fiorillo, C, Nobili, L, Malintan, NT, Zanetti, MN, Krishnakumar, SS, Lignani, G, Jepson, JEC, Broda, P, Baldassari, S, Rossi, P, Fruscione, F, Madia, F, Traverso, M, De-Marco, P, Perez-Duenas, B, Munell, F, Kriouile, Y, El-Khorassani, M, Karashova, B, Avdjieva, D, Kathom, H, Tincheva, R, Van-Maldergem, L, Nachbauer, W, Boesch, S, Gagliano, A, Amadori, E, Goraya, JS, Sultan, T, Kirmani, S, Ibrahim, S, Jan, F, Mine, J, Banu, S, Veggiotti, P, Zuccotti, G, Ferrari, MD, Van Den Maagdenberg, AMJ, Verrotti, A, Marseglia, GL, Savasta, S, Soler, MA, Scuderi, C, Borgione, E, Chimenz, R, Gitto, E, Dipasquale, V, Sallemi, A, Fusco, M, Cuppari, C, Cutrupi, MC, Ruggieri, M, Cama, A, Capra, V, Mencacci, NE, Boles, R, Gupta, N, Kabra, M, Papacostas, S, Zamba-Papanicolaou, E, Dardiotis, E, Maqbool, S, Rana, N, Atawneh, O, Lim, SY, Shaikh, F, Koutsis, G, Breza, M, Coviello, DA, Dauvilliers, YA, AlKhawaja, I, AlKhawaja, M, Al-Mutairi, F, Stojkovic, T, Ferrucci, V, Zollo, M, Alkuraya, FS, Kinali, M, Sherifa, H, Benrhouma, H, Turki, IBY, Tazir, M, Obeid, M, Bakhtadze, S, Saadi, NW, Zaki, MS, Triki, CC, Benfenati, F, Gustincich, S, Kara, M, Belcastro, V, Specchio, N, Capovilla, G, Karimiani, EG, Salih, AM, Okubadejo, NU, Ojo, OO, Oshinaike, OO, Oguntunde, O, Wahab, K, Bello, AH, Abubakar, S, Obiabo, Y, Nwazor, E, Ekenze, O, Williams, U, Iyagba, A, Taiwo, L, Komolafe, M, Senkevich, K, Shashkin, C, Zharkynbekova, N, Koneyev, K, Manizha, G, Isrofilov, M, Guliyeva, U, Salayev, K, Khachatryan, S, Rossi, S, Silvestri, G, Haridy, N, Ramenghi, LA, Xiromerisiou, G, David, E, Aguennouz, M, Fidani, L, Spanaki, C, and Tucci, A

Abstract

AMPA receptors (AMPARs) are tetrameric ligand-gated channels made up of combinations of GluA1-4 subunits encoded by GRIA1-4 genes. GluA2 has an especially important role because, following post-transcriptional editing at the Q607 site, it renders heteromultimeric AMPARs Ca2+-impermeable, with a linear relationship between current and trans-membrane voltage. Here, we report heterozygous de novo GRIA2 mutations in 28 unrelated patients with intellectual disability (ID) and neurodevelopmental abnormalities including autism spectrum disorder (ASD), Rett syndrome-like features, and seizures or developmental epileptic encephalopathy (DEE). In functional expression studies, mutations lead to a decrease in agonist-evoked current mediated by mutant subunits compared to wild-type channels. When GluA2 subunits are co-expressed with GluA1, most GRIA2 mutations cause a decreased current amplitude and some also affect voltage rectification. Our results show that de-novo variants in GRIA2 can cause neurodevelopmental disorders, complementing evidence that other genetic causes of ID, ASD and DEE also disrupt glutamatergic synaptic transmission.

Published
2019

27. Further delineation of an entity caused by CREBBP and EP300 mutations but not resembling Rubinstein-Taybi syndrome

Author

Menke, L.A., Gardeitchik, T., Hammond, P., Heimdal, K.R., Houge, G., Hufnagel, S.B., Ji, J.L., Johansson, S., Kant, S.G., Kinning, E., Leon, E.L., Newbury-Ecob, R., Paolacci, S., Pfundt, R., Ragge, N.K., Rinne, T., Ruivenkamp, C., Saitta, S.C., Sun, Y., Tartaglia, M., Terhal, P.A., Essen, A.J. van, Vigeland, M.D., Xiao, B., Hennekam, R.C., DDD Study, ARD - Amsterdam Reproduction and Development, General Paediatrics, APH - Quality of Care, and Human Genetics

Subjects
Male, Models, Anatomic, 0301 basic medicine, Microcephaly, Intellectual disability, PHENOTYPE, DISEASE, Ptosis, Missense mutation, P300, Child, Genetics (clinical), Exome sequencing, Rubinstein-Taybi Syndrome, Genetics, Sanger sequencing, EP300, Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6], Disorders of movement Donders Center for Medical Neuroscience [Radboudumc 3], CREBBP, CREB-Binding Protein, Child, Preschool, symbols, Female, medicine.symptom, Adolescent, Genotype, PROTEIN CBP, Biology, genotype-phenotype correlation, CBP, Short stature, 03 medical and health sciences, symbols.namesake, Imaging, Three-Dimensional, medicine, Humans, Genetic Predisposition to Disease, Alleles, Genetic Association Studies, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Rubinstein–Taybi syndrome, Facies, Infant, medicine.disease, 030104 developmental biology, Mutation, E1A-Associated p300 Protein, exome sequencing
Abstract

Contains fulltext : 190439.pdf (Publisher’s version ) (Closed access) In 2016, we described that missense variants in parts of exons 30 and 31 of CREBBP can cause a phenotype that differs from Rubinstein-Taybi syndrome (RSTS). Here we report on another 11 patients with variants in this region of CREBBP (between bp 5,128 and 5,614) and two with variants in the homologous region of EP300. None of the patients show characteristics typical for RSTS. The variants were detected by exome sequencing using a panel for intellectual disability in all but one individual, in whom Sanger sequencing was performed upon clinical recognition of the entity. The main characteristics of the patients are developmental delay (90%), autistic behavior (65%), short stature (42%), and microcephaly (43%). Medical problems include feeding problems (75%), vision (50%), and hearing (54%) impairments, recurrent upper airway infections (42%), and epilepsy (21%). Major malformations are less common except for cryptorchidism (46% of males), and cerebral anomalies (70%). Individuals with variants between bp 5,595 and 5,614 of CREBBP show a specific phenotype (ptosis, telecanthi, short and upslanted palpebral fissures, depressed nasal ridge, short nose, anteverted nares, short columella, and long philtrum). 3D face shape demonstrated resemblance to individuals with a duplication of 16p13.3 (the region that includes CREBBP), possibly indicating a gain of function. The other affected individuals show a less specific phenotype. We conclude that there is now more firm evidence that variants in these specific regions of CREBBP and EP300 result in a phenotype that differs from RSTS, and that this phenotype may be heterogeneous.

Published
2018

29. Truncating Variants in NAA15 Are Associated with Variable Levels of Intellectual Disability, Autism Spectrum Disorder, and Congenital Anomalies

Author

Cheng, H., Dharmadhikari, A.V., Varland, S., Ma, N., Domingo, D., Kleyner, R., Rope, A.F., Yoon, M., Stray-Pedersen, A., Posey, J.E., Crews, S.R., Eldomery, M.K., Akdemir, Z.C., Lewis, A.M., Sutton, V.R., Rosenfeld, J.A., Conboy, E., Agre, K., Xia, F., Walkiewicz, M., Longoni, M., High, F.A., Slegtenhorst, M.A. van, Mancini, G.M.S., Finnila, C.R., Haeringen, A. van, Hollander, N. den, Ruivenkamp, C., Naidu, S., Mahida, S., Palmer, E.E., Murray, L., Lim, D., Jayakar, P., Parker, M.J., Giusto, S., Stracuzzi, E., Romano, C, Beighley, J.S., Bernier, R.A., Kury, S., Nizon, M., Corbett, M.A., Shaw, M., Gardner, A., Barnett, C., Armstrong, R., Kassahn, K.S., Dijck, A. Van, Vandeweyer, G., Kleefstra, T., Schieving, J.H., Jongmans, M.C., Vries, B.B.A. de, Pfundt, R.P., Kerr, B., Rojas, S.K., Boycott, K.M., Person, R., Willaert, R., Eichler, E.E., Kooy, R.F., Yang, Y., Wu, J.C., Lupski, J.R., Arnesen, T., Cooper, G.M., Chung, W.K., Gecz, J., Stessman, H.A.F., Meng, L., Lyon, G.J., Cheng, H., Dharmadhikari, A.V., Varland, S., Ma, N., Domingo, D., Kleyner, R., Rope, A.F., Yoon, M., Stray-Pedersen, A., Posey, J.E., Crews, S.R., Eldomery, M.K., Akdemir, Z.C., Lewis, A.M., Sutton, V.R., Rosenfeld, J.A., Conboy, E., Agre, K., Xia, F., Walkiewicz, M., Longoni, M., High, F.A., Slegtenhorst, M.A. van, Mancini, G.M.S., Finnila, C.R., Haeringen, A. van, Hollander, N. den, Ruivenkamp, C., Naidu, S., Mahida, S., Palmer, E.E., Murray, L., Lim, D., Jayakar, P., Parker, M.J., Giusto, S., Stracuzzi, E., Romano, C, Beighley, J.S., Bernier, R.A., Kury, S., Nizon, M., Corbett, M.A., Shaw, M., Gardner, A., Barnett, C., Armstrong, R., Kassahn, K.S., Dijck, A. Van, Vandeweyer, G., Kleefstra, T., Schieving, J.H., Jongmans, M.C., Vries, B.B.A. de, Pfundt, R.P., Kerr, B., Rojas, S.K., Boycott, K.M., Person, R., Willaert, R., Eichler, E.E., Kooy, R.F., Yang, Y., Wu, J.C., Lupski, J.R., Arnesen, T., Cooper, G.M., Chung, W.K., Gecz, J., Stessman, H.A.F., Meng, L., and Lyon, G.J.

Abstract

Item does not contain fulltext, N-alpha-acetylation is a common co-translational protein modification that is essential for normal cell function in humans. We previously identified the genetic basis of an X-linked infantile lethal Mendelian disorder involving a c.109T>C (p.Ser37Pro) missense variant in NAA10, which encodes the catalytic subunit of the N-terminal acetyltransferase A (NatA) complex. The auxiliary subunit of the NatA complex, NAA15, is the dimeric binding partner for NAA10. Through a genotype-first approach with whole-exome or genome sequencing (WES/WGS) and targeted sequencing analysis, we identified and phenotypically characterized 38 individuals from 33 unrelated families with 25 different de novo or inherited, dominantly acting likely gene disrupting (LGD) variants in NAA15. Clinical features of affected individuals with LGD variants in NAA15 include variable levels of intellectual disability, delayed speech and motor milestones, and autism spectrum disorder. Additionally, mild craniofacial dysmorphology, congenital cardiac anomalies, and seizures are present in some subjects. RNA analysis in cell lines from two individuals showed degradation of the transcripts with LGD variants, probably as a result of nonsense-mediated decay. Functional assays in yeast confirmed a deleterious effect for two of the LGD variants in NAA15. Further supporting a mechanism of haploinsufficiency, individuals with copy-number variant (CNV) deletions involving NAA15 and surrounding genes can present with mild intellectual disability, mild dysmorphic features, motor delays, and decreased growth. We propose that defects in NatA-mediated N-terminal acetylation (NTA) lead to variable levels of neurodevelopmental disorders in humans, supporting the importance of the NatA complex in normal human development.

Published
2018

30. Truncating Variants in NAA15 Are Associated with Variable Levels of Intellectual Disability, Autism Spectrum Disorder, and Congenital Anomalies

Author

Cheng, H, Dharmadhikari, AV, Varland, S, Ma, N, Domingo, D, Kleyner, R, Rope, AF, Yoon, M, Stray-Pedersen, A, Posey, JE, Crews, SR, Eldomery, MK, Akdemir, ZC, Lewis, AM, Sutton, VR, Rosenfeld, JA, Conboy, E, Agre, K, Xia, F, Walkiewicz, M, Longoni, M, High, FA, van Slegtenhorst, MA, Mancini, GMS, Finnila, CR, van Haeringen, A, den Hollander, N, Ruivenkamp, C, Naidu, S, Mahida, S, Palmer, EE, Murray, L, Lim, D, Jayakar, P, Parker, MJ, Giusto, S, Stracuzzi, E, Romano, C, Beighley, JS, Bernier, RA, Küry, S, Nizon, M, Corbett, MA, Shaw, M, Gardner, A, Barnett, C, Armstrong, R, Kassahn, KS, Van Dijck, A, Vandeweyer, G, Kleefstra, T, Schieving, J, Jongmans, MJ, de Vries, BBA, Pfundt, R, Kerr, B, Rojas, SK, Boycott, KM, Person, R, Willaert, R, Eichler, EE, Kooy, RF, Yang, Y, Wu, JC, Lupski, JR, Arnesen, T, Cooper, GM, Chung, WK, Gecz, J, Stessman, HAF, Meng, L, Lyon, GJ, Cheng, H, Dharmadhikari, AV, Varland, S, Ma, N, Domingo, D, Kleyner, R, Rope, AF, Yoon, M, Stray-Pedersen, A, Posey, JE, Crews, SR, Eldomery, MK, Akdemir, ZC, Lewis, AM, Sutton, VR, Rosenfeld, JA, Conboy, E, Agre, K, Xia, F, Walkiewicz, M, Longoni, M, High, FA, van Slegtenhorst, MA, Mancini, GMS, Finnila, CR, van Haeringen, A, den Hollander, N, Ruivenkamp, C, Naidu, S, Mahida, S, Palmer, EE, Murray, L, Lim, D, Jayakar, P, Parker, MJ, Giusto, S, Stracuzzi, E, Romano, C, Beighley, JS, Bernier, RA, Küry, S, Nizon, M, Corbett, MA, Shaw, M, Gardner, A, Barnett, C, Armstrong, R, Kassahn, KS, Van Dijck, A, Vandeweyer, G, Kleefstra, T, Schieving, J, Jongmans, MJ, de Vries, BBA, Pfundt, R, Kerr, B, Rojas, SK, Boycott, KM, Person, R, Willaert, R, Eichler, EE, Kooy, RF, Yang, Y, Wu, JC, Lupski, JR, Arnesen, T, Cooper, GM, Chung, WK, Gecz, J, Stessman, HAF, Meng, L, and Lyon, GJ

Abstract

N-alpha-acetylation is a common co-translational protein modification that is essential for normal cell function in humans. We previously identified the genetic basis of an X-linked infantile lethal Mendelian disorder involving a c.109T>C (p.Ser37Pro) missense variant in NAA10, which encodes the catalytic subunit of the N-terminal acetyltransferase A (NatA) complex. The auxiliary subunit of the NatA complex, NAA15, is the dimeric binding partner for NAA10. Through a genotype-first approach with whole-exome or genome sequencing (WES/WGS) and targeted sequencing analysis, we identified and phenotypically characterized 38 individuals from 33 unrelated families with 25 different de novo or inherited, dominantly acting likely gene disrupting (LGD) variants in NAA15. Clinical features of affected individuals with LGD variants in NAA15 include variable levels of intellectual disability, delayed speech and motor milestones, and autism spectrum disorder. Additionally, mild craniofacial dysmorphology, congenital cardiac anomalies, and seizures are present in some subjects. RNA analysis in cell lines from two individuals showed degradation of the transcripts with LGD variants, probably as a result of nonsense-mediated decay. Functional assays in yeast confirmed a deleterious effect for two of the LGD variants in NAA15. Further supporting a mechanism of haploinsufficiency, individuals with copy-number variant (CNV) deletions involving NAA15 and surrounding genes can present with mild intellectual disability, mild dysmorphic features, motor delays, and decreased growth. We propose that defects in NatA-mediated N-terminal acetylation (NTA) lead to variable levels of neurodevelopmental disorders in humans, supporting the importance of the NatA complex in normal human development.

Published
2018

31. Targeted sequencing identifies 91 neurodevelopmental-disorder risk genes with autism and developmental-disability biases

Author

Stessman, H.A., Xiong, B., Coe, B.P., Wang, T., Hoekzema, K., Fenckova, M., Kvarnung, M., Gerdts, J., Trinh, S., Cosemans, N., Vives, L., Lin, J., Turner, T.N., Santen, G., Ruivenkamp, C., Kriek, M., Haeringen, A. van, Aten, E., Friend, K., Liebelt, J., Barnett, C., Haan, E., Shaw, M., Gecz, J., Anderlid, B.M., Nordgren, A., Lindstrand, A., Schwartz, C., Kooy, R.F., Vandeweyer, G., Helsmoortel, C., Romano, C, Alberti, A., Vinci, M., Avola, E., Giusto, S., Courchesne, E., Pramparo, T., Pierce, K., Nalabolu, S., Amaral, D.G., Scheffer, I.E., Delatycki, M.B., Lockhart, P.J., Hormozdiari, F., Harich, B., Castells Nobau, A., Xia, K., Peeters, H., Nordenskjold, M., Schenck, A., Bernier, R.A., Eichler, E.E., Stessman, H.A., Xiong, B., Coe, B.P., Wang, T., Hoekzema, K., Fenckova, M., Kvarnung, M., Gerdts, J., Trinh, S., Cosemans, N., Vives, L., Lin, J., Turner, T.N., Santen, G., Ruivenkamp, C., Kriek, M., Haeringen, A. van, Aten, E., Friend, K., Liebelt, J., Barnett, C., Haan, E., Shaw, M., Gecz, J., Anderlid, B.M., Nordgren, A., Lindstrand, A., Schwartz, C., Kooy, R.F., Vandeweyer, G., Helsmoortel, C., Romano, C, Alberti, A., Vinci, M., Avola, E., Giusto, S., Courchesne, E., Pramparo, T., Pierce, K., Nalabolu, S., Amaral, D.G., Scheffer, I.E., Delatycki, M.B., Lockhart, P.J., Hormozdiari, F., Harich, B., Castells Nobau, A., Xia, K., Peeters, H., Nordenskjold, M., Schenck, A., Bernier, R.A., and Eichler, E.E.

Abstract

Item does not contain fulltext, Gene-disruptive mutations contribute to the biology of neurodevelopmental disorders (NDDs), but most of the related pathogenic genes are not known. We sequenced 208 candidate genes from >11,730 cases and >2,867 controls. We identified 91 genes, including 38 new NDD genes, with an excess of de novo mutations or private disruptive mutations in 5.7% of cases. Drosophila functional assays revealed a subset with increased involvement in NDDs. We identified 25 genes showing a bias for autism versus intellectual disability and highlighted a network associated with high-functioning autism (full-scale IQ >100). Clinical follow-up for NAA15, KMT5B, and ASH1L highlighted new syndromic and nonsyndromic forms of disease.

Published
2017

32. Targeted sequencing identifies 91 neurodevelopmental-disorder risk genes with autism and developmental-disability biases

Author

Stessman, HAF, Xiong, B, Coe, BP, Wang, T, Hoekzema, K, Fenckova, M, Kvarnung, M, Gerdts, J, Trinh, S, Cosemans, N, Vives, L, Lin, J, Turner, TN, Santen, G, Ruivenkamp, C, Kriek, M, van Haeringen, A, Aten, E, Friend, K, Liebelt, J, Barnett, C, Haan, E, Shaw, M, Gecz, J, Anderlid, B-M, Nordgren, A, Lindstrand, A, Schwartz, C, Kooy, RF, Vandeweyer, G, Helsmoortel, C, Romano, C, Alberti, A, Vinci, M, Avola, E, Giusto, S, Courchesne, E, Pramparo, T, Pierce, K, Nalabolu, S, Amaral, DG, Scheffer, IE, Delatycki, MB, Lockhart, PJ, Hormozdiari, F, Harich, B, Castells-Nobau, A, Xia, K, Peeters, H, Nordenskjold, M, Schenck, A, Bernier, RA, Eichler, EE, Stessman, HAF, Xiong, B, Coe, BP, Wang, T, Hoekzema, K, Fenckova, M, Kvarnung, M, Gerdts, J, Trinh, S, Cosemans, N, Vives, L, Lin, J, Turner, TN, Santen, G, Ruivenkamp, C, Kriek, M, van Haeringen, A, Aten, E, Friend, K, Liebelt, J, Barnett, C, Haan, E, Shaw, M, Gecz, J, Anderlid, B-M, Nordgren, A, Lindstrand, A, Schwartz, C, Kooy, RF, Vandeweyer, G, Helsmoortel, C, Romano, C, Alberti, A, Vinci, M, Avola, E, Giusto, S, Courchesne, E, Pramparo, T, Pierce, K, Nalabolu, S, Amaral, DG, Scheffer, IE, Delatycki, MB, Lockhart, PJ, Hormozdiari, F, Harich, B, Castells-Nobau, A, Xia, K, Peeters, H, Nordenskjold, M, Schenck, A, Bernier, RA, and Eichler, EE

Abstract

Gene-disruptive mutations contribute to the biology of neurodevelopmental disorders (NDDs), but most of the related pathogenic genes are not known. We sequenced 208 candidate genes from >11,730 cases and >2,867 controls. We identified 91 genes, including 38 new NDD genes, with an excess of de novo mutations or private disruptive mutations in 5.7% of cases. Drosophila functional assays revealed a subset with increased involvement in NDDs. We identified 25 genes showing a bias for autism versus intellectual disability and highlighted a network associated with high-functioning autism (full-scale IQ >100). Clinical follow-up for NAA15, KMT5B, and ASH1L highlighted new syndromic and nonsyndromic forms of disease.

Published
2017

33. A Dutch MYH7 founder mutation, p.(Asn1918Lys), is associated with early onset cardiomyopathy and congenital heart defects

Author

van der Linde, IHM, Hiemstra, YL, Bokenkamp, R, Mil, Annemieke, Breuning, MH, Ruivenkamp, C, ten Broeke, SW, Veldkamp, RF, Waning, Jaap, van Slegtenhorst, MA, Spaendonck-Zwarts, KY, Deprez, RHL, Herkert, JC, Boven, LA, van der Zwaag, PA, Jongbloed, JDH, Bootsma, M, Barge-Schaapveld, D, van der Linde, IHM, Hiemstra, YL, Bokenkamp, R, Mil, Annemieke, Breuning, MH, Ruivenkamp, C, ten Broeke, SW, Veldkamp, RF, Waning, Jaap, van Slegtenhorst, MA, Spaendonck-Zwarts, KY, Deprez, RHL, Herkert, JC, Boven, LA, van der Zwaag, PA, Jongbloed, JDH, Bootsma, M, and Barge-Schaapveld, D

Published
2017

35. Rothmund-Thomson syndrome and osteoma cutis in a patient previously diagnosed as COPS syndrome.

Author

Rij, M., Grijsen, M., Appelman-Dijkstra, N., Hansson, K., Ruivenkamp, C., Mulder, K., Doorn, R., Oranje, A., Kant, S., van Rij, M C, Grijsen, M L, Appelman-Dijkstra, N M, Hansson, K B M, Ruivenkamp, C A L, van Doorn, R, Oranje, A P, and Kant, S G

Subjects
ROTHMUND-Thomson syndrome, SYMPTOMS, BONE densitometry, PHYSICAL diagnosis, CYTOGENETICS, HODGKIN'S disease, BONE abnormalities, GENETIC disorder diagnosis, LYMPHOMA diagnosis, OSTEOPENIA, OSTEOPOROSIS diagnosis, SKIN disease diagnosis, METAPLASTIC ossification, CALCINOSIS, CHROMOSOME abnormalities, CHROMOSOMES, DIAGNOSIS, MEDICAL errors, PEOPLE with intellectual disabilities, SYNDROMES
Abstract

We present a patient with poikiloderma, severe osteoporosis and a mild intellectual disability. At the age of 9 years, this patient was proposed to suffer from a novel disease entity designated as calcinosis cutis, osteoma cutis, poikiloderma and skeletal abnormalities (COPS) syndrome. At the age of 35, he was diagnosed with Hodgkin's lymphoma. Recently, biallelic pathogenic variants in the RECQL4 gene were detected (c.1048_1049delAG and c.1391-1G>A), confirming a diagnosis of Rothmund-Thomson syndrome (RTS). In the brother of this patient, who had a milder phenotype, a similar diagnosis was made.Conclusion: We conclude that COPS syndrome never existed as a separate syndrome entity. Instead, osteoma cutis may be regarded as a novel feature of RTS, whereas mild intellectual disability and lymphoma may be underreported parts of the phenotype. What is new: • Osteoma cutis was not a known feature in Rothmund-Thomson patients. • Intellectual disability may be considered a rare feature in RTS; more study is needed. What is known: • RTS is a well-described syndrome caused by mutations in the RECQL4 gene. • Patients with RTS frequently show chromosomal abnormalities like, e.g. mosaic trisomy 8. [ABSTRACT FROM AUTHOR]

Published
2017
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37. DNA Methylation Profiling of Uniparental Disomy Subjects Provides a Map of Parental Epigenetic Bias in the Human Genome

Author

Joshi, R.S., Garg, P., Zaitlen, N., Lappalainen, T., Watson, C.T., Azam, N., Ho, D., Li, X., Antonarakis, S.E., Brunner, H.G., Buiting, K., Cheung, S.W., Coffee, B., Eggermann, T., Francis, D., Geraedts, J.P., Gimelli, G., Jacobson, S.G., Le Caignec, C., Leeuw, N. de, Liehr, T., Mackay, D.J., Montgomery, S.B., Pagnamenta, A.T., Papenhausen, P., Robinson, D.O., Ruivenkamp, C., Schwartz, C., Steiner, B., Stevenson, D.A., Surti, U., Wassink, T., Sharp, A.J., Joshi, R.S., Garg, P., Zaitlen, N., Lappalainen, T., Watson, C.T., Azam, N., Ho, D., Li, X., Antonarakis, S.E., Brunner, H.G., Buiting, K., Cheung, S.W., Coffee, B., Eggermann, T., Francis, D., Geraedts, J.P., Gimelli, G., Jacobson, S.G., Le Caignec, C., Leeuw, N. de, Liehr, T., Mackay, D.J., Montgomery, S.B., Pagnamenta, A.T., Papenhausen, P., Robinson, D.O., Ruivenkamp, C., Schwartz, C., Steiner, B., Stevenson, D.A., Surti, U., Wassink, T., and Sharp, A.J.

Abstract

Contains fulltext : 167696.pdf (Publisher’s version ) (Closed access), Genomic imprinting is a mechanism in which gene expression varies depending on parental origin. Imprinting occurs through differential epigenetic marks on the two parental alleles, with most imprinted loci marked by the presence of differentially methylated regions (DMRs). To identify sites of parental epigenetic bias, here we have profiled DNA methylation patterns in a cohort of 57 individuals with uniparental disomy (UPD) for 19 different chromosomes, defining imprinted DMRs as sites where the maternal and paternal methylation levels diverge significantly from the biparental mean. Using this approach we identified 77 DMRs, including nearly all those described in previous studies, in addition to 34 DMRs not previously reported. These include a DMR at TUBGCP5 within the recurrent 15q11.2 microdeletion region, suggesting potential parent-of-origin effects associated with this genomic disorder. We also observed a modest parental bias in DNA methylation levels at every CpG analyzed across approximately 1.9 Mb of the 15q11-q13 Prader-Willi/Angelman syndrome region, demonstrating that the influence of imprinting is not limited to individual regulatory elements such as CpG islands, but can extend across entire chromosomal domains. Using RNA-seq data, we detected signatures consistent with imprinted expression associated with nine novel DMRs. Finally, using a population sample of 4,004 blood methylomes, we define patterns of epigenetic variation at DMRs, identifying rare individuals with global gain or loss of methylation across multiple imprinted loci. Our data provide a detailed map of parental epigenetic bias in the human genome, providing insights into potential parent-of-origin effects.

Published
2016

38. Monosomy 18p: Risks for developing FSHD

Author

Goossens, R., primary, Balog, J., additional, Lemmers, J., additional, van den Boogaard, M., additional, van der Vliet, P., additional, Donlin-Smith, C., additional, Nations, S., additional, Kriek, M., additional, Ruivenkamp, C., additional, Heard, P., additional, Bakker, B., additional, Tapscott, S., additional, Cody, J., additional, Tawil, R., additional, and van der Maarel, S., additional

Published
2016
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39. Heterozygous Loss-of-Function Mutations in DLL4 Cause Adams-Oliver Syndrome

Author

Meester, J.A., Southgate, L., Stittrich, A.B., Venselaar, H., Beekmans, S.J., Hollander, N. den, Bijlsma, E.K., Helderman-van den Enden, A.T., Verheij, J.B., Glusman, G., Roach, J.C., Lehman, A., Patel, M.S., Vries, B. de, Ruivenkamp, C., Itin, P., Prescott, K., Clarke, S., Trembath, R., Zenker, M., Sukalo, M., Laer, L. Van, Loeys, B.L., Wuyts, W., Meester, J.A., Southgate, L., Stittrich, A.B., Venselaar, H., Beekmans, S.J., Hollander, N. den, Bijlsma, E.K., Helderman-van den Enden, A.T., Verheij, J.B., Glusman, G., Roach, J.C., Lehman, A., Patel, M.S., Vries, B. de, Ruivenkamp, C., Itin, P., Prescott, K., Clarke, S., Trembath, R., Zenker, M., Sukalo, M., Laer, L. Van, Loeys, B.L., and Wuyts, W.

Abstract

Contains fulltext : 152973.pdf (publisher's version ) (Closed access), Adams-Oliver syndrome (AOS) is a rare developmental disorder characterized by the presence of aplasia cutis congenita (ACC) of the scalp vertex and terminal limb-reduction defects. Cardiovascular anomalies are also frequently observed. Mutations in five genes have been identified as a cause for AOS prior to this report. Mutations in EOGT and DOCK6 cause autosomal-recessive AOS, whereas mutations in ARHGAP31, RBPJ, and NOTCH1 lead to autosomal-dominant AOS. Because RBPJ, NOTCH1, and EOGT are involved in NOTCH signaling, we hypothesized that mutations in other genes involved in this pathway might also be implicated in AOS pathogenesis. Using a candidate-gene-based approach, we prioritized DLL4, a critical NOTCH ligand, due to its essential role in vascular development in the context of cardiovascular features in AOS-affected individuals. Targeted resequencing of the DLL4 gene with a custom enrichment panel in 89 independent families resulted in the identification of seven mutations. A defect in DLL4 was also detected in two families via whole-exome or genome sequencing. In total, nine heterozygous mutations in DLL4 were identified, including two nonsense and seven missense variants, the latter encompassing four mutations that replace or create cysteine residues, which are most likely critical for maintaining structural integrity of the protein. Affected individuals with DLL4 mutations present with variable clinical expression with no emerging genotype-phenotype correlations. Our findings demonstrate that DLL4 mutations are an additional cause of autosomal-dominant AOS or isolated ACC and provide further evidence for a key role of NOTCH signaling in the etiology of this disorder.

Published
2015

40. Risk of erroneous results in carrier testing for haemophilia A without prior DNA analysis in male index patients

Author

Genetica Klinische Genetica, Fransen van de Putte, D. E., Frankhuizen, W. S., Vijfhuizen, L., Groenewegen, L., Tamminga, R. Y J, Bouman, K., van Essen, A. J., Gijsbers, A. C J, Ruivenkamp, C. A L, Boon, E. M J, Genetica Klinische Genetica, Fransen van de Putte, D. E., Frankhuizen, W. S., Vijfhuizen, L., Groenewegen, L., Tamminga, R. Y J, Bouman, K., van Essen, A. J., Gijsbers, A. C J, Ruivenkamp, C. A L, and Boon, E. M J

Published
2015

41. A Dutch MYH7 founder mutation, p.(Asn1918Lys), is associated with early onset cardiomyopathy and congenital heart defects.

Author

Linde, I., Hiemstra, Y., Bökenkamp, R., Mil, A., Breuning, M., Ruivenkamp, C., Broeke, S., Veldkamp, R., Waning, J., Slegtenhorst, M., Spaendonck-Zwarts, K., Lekanne Deprez, R., Herkert, J., Boven, L., Zwaag, P., Jongbloed, J., Bootsma, M., and Barge-Schaapveld, D.

Subjects
GENETIC mutation, CARDIOMYOPATHIES, CONGENITAL heart disease, DEFIBRILLATORS, HAPLOTYPES
Abstract

Background: Mutations in the myosin heavy chain 7 ( MYH7) gene commonly cause cardiomyopathy but are less frequently associated with congenital heart defects. Methods: In this study, we describe a mutation in the MYH7 gene, c. 5754C > G; p. (Asn1918Lys), present in 15 probands and 65 family members. Results: Of the 80 carriers (age range 0-88 years), 46 (57.5%) had cardiomyopathy (mainly dilated cardiomyopathy (DCM)) and seven (8.8%) had a congenital heart defect. Childhood onset of cardiomyopathy was present in almost 10% of carriers. However, in only a slight majority (53.7%) was the left ventricular ejection fraction reduced and almost no arrhythmias or conduction disorders were noted. Moreover, only one carrier required heart transplantation and nine (11.3%) an implantable cardioverter defibrillator. In addition, the standardised mortality ratio for MYH7 carriers was not significantly increased. Whole exome sequencing in several cases with paediatric onset of DCM and one with isolated congenital heart defects did not reveal additional known disease-causing variants. Haplotype analysis suggests that the MYH7 variant is a founder mutation, and is therefore the first Dutch founder mutation identified in the MYH7 gene. The mutation appears to have originated in the western region of the province of South Holland between 500 and 900 years ago. Conclusion: Clinically, the p. (Asn1918Lys) mutation is associated with congenital heart defects and/or cardiomyopathy at young age but with a relatively benign course. [ABSTRACT FROM AUTHOR]

Published
2017
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42. Xq28 duplications including MECP2 in five females: Expanding the phenotype to severe mental retardation

Author

Bijlsma, E. K., Collins, A., Papa, F. T., Tejada, M. I., Wheeler, P., Peeters, E. A., Gijsbers, A. C., van de Kamp, J. M., Kriek, M., Losekoot, M., Broekma, A. J., Crolla, J. A., Pollazzon, M., Mucciolo, M., Katzaki, E., Disciglio, V., Ferreri, M. I., Marozza, A., Mencarelli, M. A., Castagnini, C., Dosa, L., Ariani, Francesca, Mari, Francesca, Canitano, R., Hayek, G., Botella, M. P., Gener, B., Mínguez, M., Renieri, Alessandra, Ruivenkamp, C. A., and Papa, FILOMENA TIZIANA

Subjects
congenital, hereditary, and neonatal diseases and abnormalities, Methyl-CpG-Binding Protein 2, MECP2 duplication syndrome, Chromosomal translocation, Biology, IRAK1, X-inactivation, MECP2, MECP2 duplication, X Chromosome Inactivation, Clinical Research, Intellectual Disability, Chromosome Duplication, Gene duplication, Genetics, medicine, Humans, Abnormalities, Multiple, Child, Genetic Association Studies, Genetics (clinical), Chromosomes, Human, X, Chromosome, Karyotype, General Medicine, medicine.disease, Chromosome Banding, Pedigree, nervous system diseases, Xq28, Phenotype, Xq28 duplication, Female, Mental retardation in females
Abstract

Duplications leading to functional disomy of chromosome Xq28, including MECP2 as the critical dosage-sensitive gene, are associated with a distinct clinical phenotype in males, characterized by severe mental retardation, infantile hypotonia, progressive neurologic impairment, recurrent infections, bladder dysfunction, and absent speech. Female patients with Xq duplications including MECP2 are rare. Only recently submicroscopic duplications of this region on Xq28 have been recognized in four females, and a triplication in a fifth, all in combination with random X-chromosome inactivation (XCI). Based on this small series, it was concluded that in females with MECP2 duplication and random XCI, the typical symptoms of affected boys are not present. We present clinical and molecular data on a series of five females with an Xq28 duplication including the MECP2 gene, both isolated and as the result of a translocation, and compare them with the previously reported cases of small duplications in females. The collected data indicate that the associated phenotype in females is distinct from males with similar duplications, but the clinical effects may be as severe as seen in males.

Published
2012

43. Thrombocytopenia with Absent Radii (TAR) syndrome is cause by compound inheritance of low-frequency regulatory SNPs and a rare null mutation in exon-junction complex subunit RBM8A

Author

Albers, C. A., Paul, D. S., Schulze, H., Freson, K., Stephens, J. C., Smethurst, P. A., Jolley, J. D., Cvejic, A., Kostadima, M., Paul Bertone, Breuning, M. H., Debili, N., Deloukas, P., Favier, R., Fiedler, J., Hobbs, C. M., Huang, N., Hurles, M. E., Kiddle, G., Krapels, I., Nurden, P., Ruivenkamp, C. A. L., Sambrook, J. G., Smith, K., Stemple, D. L., Strauss, G., Thys, C., Geet, C., Newbury-Ecob, R., Ouwehand, W. H., and Ghevaert, C.

Published
2012

44. Central 22q11.2 deletions

Author

Rump, P., Leeuw, N. de, Essen, A.J. van, Verschuuren-Bemelmans, C.C., Veenstra-Knol, H.E., Swinkels, M.E., Oostdijk, W., Ruivenkamp, C., Reardon, W., Munnik, S. de, Ruiter, M., Frumkin, A., Lev, D., Evers, C., Sikkema-Raddatz, B., Dijkhuizen, T., Ravenswaaij-Arts, C.M.A. van, Rump, P., Leeuw, N. de, Essen, A.J. van, Verschuuren-Bemelmans, C.C., Veenstra-Knol, H.E., Swinkels, M.E., Oostdijk, W., Ruivenkamp, C., Reardon, W., Munnik, S. de, Ruiter, M., Frumkin, A., Lev, D., Evers, C., Sikkema-Raddatz, B., Dijkhuizen, T., and Ravenswaaij-Arts, C.M.A. van

Abstract

Item does not contain fulltext, 22q11.2 deletion syndrome is one of the most common microdeletion syndromes. Most patients have a deletion resulting from a recombination of low copy repeat blocks LCR22-A and LCR22-D. Loss of the TBX1 gene is considered the most important cause of the phenotype. A limited number of patients with smaller, overlapping deletions distal to the TBX1 locus have been described in the literature. In these patients, the CRKL gene is deleted. Haploinsufficiency of this gene has also been implicated in the pathogenesis of 22q11.2 deletion syndrome. To distinguish these deletions (comprising the LCR22-B to LCR22-D region) from the more distal 22q11.2 deletions (located beyond LCR22-D), we propose the term "central 22q11.2 deletions". In the present study we report on 27 new patients with such a deletion. Together with information on previously published cases, we review the clinical findings of 52 patients. The prevalence of congenital heart anomalies and the frequency of de novo deletions in patients with a central deletion are substantially lower than in patients with a common or distal 22q11.2 deletion. Renal and urinary tract malformations, developmental delays, cognitive impairments and behavioral problems seem to be equally frequent as in patients with a common deletion. None of the patients had a cleft palate. Patients with a deletion that also encompassed the MAPK1 gene, located just distal to LCR22-D, have a different and more severe phenotype, characterized by a higher prevalence of congenital heart anomalies, growth restriction and microcephaly. Our results further elucidate genotype-phenotype correlations in 22q11.2 deletion syndrome spectrum.

Published
2014

46. Intragenic deletion in DYRK1A leads to mental retardation and primary microcephaly

Author

Bon, B.W. van, Hoischen, A., Hehir-Kwa, J.Y., Brouwer, A.P. de, Ruivenkamp, C., Gijsbers, A.C.J., Marcelis, C.L.M., Leeuw, N. de, Veltman, J.A., Brunner, H.G., Vries, L.B.A. de, Bon, B.W. van, Hoischen, A., Hehir-Kwa, J.Y., Brouwer, A.P. de, Ruivenkamp, C., Gijsbers, A.C.J., Marcelis, C.L.M., Leeuw, N. de, Veltman, J.A., Brunner, H.G., and Vries, L.B.A. de

Abstract

Contains fulltext : 97061.pdf (Publisher’s version ) (Closed access)

Published
2011

47. P.265 - Monosomy 18p: Risks for developing FSHD

Author

Goossens, R., Balog, J., Lemmers, J., van den Boogaard, M., van der Vliet, P., Donlin-Smith, C., Nations, S., Kriek, M., Ruivenkamp, C., Heard, P., Bakker, B., Tapscott, S., Cody, J., Tawil, R., and van der Maarel, S.

Published
2016
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48. Array analysis and karyotyping: workflow consequences based on a retrospective study of 36,325 patients with idiopathic developmental delay in the Netherlands.

Author

Hochstenbach, R., Binsbergen, E. van, Engelen, J., Nieuwint, A.W., Polstra, A., Poddighe, P.J., Ruivenkamp, C., Sikkema-Raddatz, B., Smeets, D.F.C.M., Poot, M., Hochstenbach, R., Binsbergen, E. van, Engelen, J., Nieuwint, A.W., Polstra, A., Poddighe, P.J., Ruivenkamp, C., Sikkema-Raddatz, B., Smeets, D.F.C.M., and Poot, M.

Abstract

Item does not contain fulltext, Anomalies of chromosome number and structure are considered to be the most frequent cause of unexplained, non-syndromic developmental delay and mental retardation (DD/MR). High-resolution, genome-wide, array-based segmental aneusomy profiling has emerged as a highly sensitive technique for detecting pathogenic genomic imbalances. A review of 29 array-based studies of DD/MR patients showed that a yield of at least approximately 19% pathogenic aberrations is attainable in unselected, consecutive DD/MR referrals if array platforms with 30-70 kb median probe spacing are used as an initial genetic testing method. This corresponds to roughly twice the rate of classical cytogenetics. This raises the question whether chromosome banding studies, combined with targeted approaches, such as fluorescence in situ hybridisation for the detection of microdeletions, still hold substantial relevance for the clinical investigation of these patients. To address this question, we reviewed the outcome of cytogenetic studies in all 36,325 DD/MR referrals in the Netherlands during the period 1996-2005, a period before the advent of array-based genome investigation. We estimate that in a minimum of 0.78% of all referrals a balanced chromosomal rearrangement would have remained undetected by array-based investigation. These include familial rearrangements (0.48% of all referrals), de novo reciprocal translocations and inversions (0.23% of all referrals), de novo Robertsonian translocations (0.04% of all referrals), and 69,XXX triploidy (0.03% of all referrals). We conclude that karyotyping, following an initial array-based investigation, would give only a limited increase in the number of pathogenic abnormalities, i.e. 0.23% of all referrals with a de novo, apparently balanced, reciprocal translocation or inversion (assuming that all of these are pathogenic), and 0.03% of all referrals with 69,XXX triploidy. We propose that, because of its high diagnostic yield, high-resolution array-based g

Published
2009

49. Extending the phenotype of recurrent rearrangements of 16p11.2: deletions in mentally retarded patients without autism and in normal individuals.

Author

Bijlsma, E.K., Gijsbers, A.C.J., Schuurs-Hoeijmakers, J.H.M., Haeringen, A. van, Fransen van de Putte, D.E., Anderlid, B.M., Lundin, J., Lapunzina, P., Perez Jurado, L.A., Chiaie, B. Delle, Loeys, B.L., Menten, B., Oostra, A., Verhelst, H., Amor, D.J., Bruno, D.L., Essen, A.J. van, Hordijk, R., Sikkema-Raddatz, B., Verbruggen, K.T., Jongmans, M.C.J., Pfundt, R.P., Reeser, H.M., Breuning, M.H., Ruivenkamp, C., Bijlsma, E.K., Gijsbers, A.C.J., Schuurs-Hoeijmakers, J.H.M., Haeringen, A. van, Fransen van de Putte, D.E., Anderlid, B.M., Lundin, J., Lapunzina, P., Perez Jurado, L.A., Chiaie, B. Delle, Loeys, B.L., Menten, B., Oostra, A., Verhelst, H., Amor, D.J., Bruno, D.L., Essen, A.J. van, Hordijk, R., Sikkema-Raddatz, B., Verbruggen, K.T., Jongmans, M.C.J., Pfundt, R.P., Reeser, H.M., Breuning, M.H., and Ruivenkamp, C.

Abstract

Contains fulltext : 80707.pdf (publisher's version ) (Closed access), Array CGH (comparative genomic hybridization) screening of large patient cohorts with mental retardation and/or multiple congenital anomalies (MR/MCA) has led to the identification of a number of new microdeletion and microduplication syndromes. Recently, a recurrent copy number variant (CNV) at chromosome 16p11.2 was reported to occur in up to 1% of autistic patients in three large autism studies. In the screening of 4284 patients with MR/MCA with various array platforms, we detected 22 individuals (14 index patients and 8 family members) with deletions in 16p11.2, which are genomically identical to those identified in the autism studies. Though some patients shared a facial resemblance and a tendency to overweight, there was no evidence for a recognizable phenotype. Autism was not the presenting feature in our series. The assembled evidence indicates that recurrent 16p11.2 deletions are associated with variable clinical outcome, most likely arising from haploinsufficiency of one or more genes. The phenotypical spectrum ranges from MR and/or MCA, autism, learning and speech problems, to a normal phenotype.

Published
2009

50. Split hand-foot malformation, tetralogy of Fallot, mental retardation and a 1 Mb 19p deletion-evidence for further heterogeneity?

Author

Aten, E., Hollander, N. den, Ruivenkamp, C., Knijnenburg, J., Bokhoven, J.H.L.M. van, Dunnen, J. den, Breuning, M., Aten, E., Hollander, N. den, Ruivenkamp, C., Knijnenburg, J., Bokhoven, J.H.L.M. van, Dunnen, J. den, and Breuning, M.

Abstract

Contains fulltext : 81477.pdf (publisher's version ) (Closed access), Congenital limb malformations are the second most common birth defects observed in infants. Split hand foot malformation (SHFM), also known as central ray deficiency, ectrodactyly and cleft hand/foot, occurs isolated or in combination with other malformations. We report on a male patient with SHFM, tetralogy of Fallot and a clinical phenotype suggestive of Angelman syndrome. Using array based genome analysis (3K BACs and 500K SNPs), we identified a de novo deletion of chromosome 19p13.11, confirmed by Fluorescent In Situ Hybridization analysis. The deletion is 0.99 Mb in size and contains 28 genes. The proximal breakpoint of the deletion is in EPS15L1, which may be involved in vertebrate limb development. Subsequent screening of 21 syndromic and nonsyndromic SHFM patients (TP73L mutation negative) for rearrangements using Multiplex Ligation-dependent Probe Amplification did not detect other deletions or duplications in chromosome 19. These findings suggest that our patient may have a new contiguous gene syndrome and indicates that SHFM is genetically more heterogeneous than currently known.

Published
2009

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