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2. Consensus recommendations on organization of care for individuals with Phelan-McDermid syndrome

Author

Gaasterland, C.M.W., Klein Haneveld, M.J., Vyshka, Klea, Hugon, A., van Eeghen, A.M., Alhambra, Norma, Anderlid, Britt-Marie, Andres, Stephanie, Aten, Emmelien, Guedes, Rui Barbosa, Bonaglia, Maria C., Bourgeron, Thomas, Burdeus-Olavarrieta, Monica, Carbin, Maya J., Cooke, Jennifer, Damstra, Robert J., de Coo, Irenaeus F.M., Di Domenico, Stella, Evans, D. Gareth, Fernández-Fructuoso, José Ramón, Grabrucker, Andreas M., Gunnarson, Cecilia, Hadzsiev, Kinga, Hennekam, Raoul C., Jesse, Sarah, Kant, Sarina G., Koza, Sylvia A., Kuiper, Els, Landlust, Annemiek M., Lapunzina, Pablo, Loth, Eva, Mansour, Sahar, Maruani, Anna, Mattina, Teresa, Matulevičienė, Aušra, Nevado, Julián, Parker, Susanne, Robert, Sandra, Sala, Carlo, San José Cáceres, Antonia, Schön, Michael, Šiaurytė, Kamilė, Stemkens, Daphne, Stiefsohn, Dominique, Swillen, Ann, Tabet, Anne C., Toro, Roberto, Turner, Alison, van Balkom, Ingrid D.C., van Buggenhout, Griet, van Eeghen, Agnies M., van Ravenswaaij-Arts, Conny M.A., van Weering, Sabrina, Verpelli, Chiara, Vignes, Stephane, Vogels, Annick, Walinga, Margreet, Stemkens, D., Maruani, A., Hadzsiev, K., and van Balkom, I.D.C.

Published
2023
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4. The clinical and molecular spectrum of the KDM6B-related neurodevelopmental disorder

Author

Rots, Dmitrijs, Jakub, Taryn E., Keung, Crystal, Jackson, Adam, Banka, Siddharth, Pfundt, Rolph, de Vries, Bert B.A., van Jaarsveld, Richard H., Hopman, Saskia M.J., van Binsbergen, Ellen, Valenzuela, Irene, Hempel, Maja, Bierhals, Tatjana, Kortüm, Fanny, Lecoquierre, Francois, Goldenberg, Alice, Hertz, Jens Michael, Andersen, Charlotte Brasch, Kibæk, Maria, Prijoles, Eloise J., Stevenson, Roger E., Everman, David B., Patterson, Wesley G., Meng, Linyan, Gijavanekar, Charul, De Dios, Karl, Lakhani, Shenela, Levy, Tess, Wagner, Matias, Wieczorek, Dagmar, Benke, Paul J., Lopez Garcia, María Soledad, Perrier, Renee, Sousa, Sergio B., Almeida, Pedro M., Simões, Maria José, Isidor, Bertrand, Deb, Wallid, Schmanski, Andrew A., Abdul-Rahman, Omar, Philippe, Christophe, Bruel, Ange-Line, Faivre, Laurence, Vitobello, Antonio, Thauvin, Christel, Smits, Jeroen J., Garavelli, Livia, Caraffi, Stefano G., Peluso, Francesca, Davis-Keppen, Laura, Platt, Dylan, Royer, Erin, Leeuwen, Lisette, Sinnema, Margje, Stegmann, Alexander P.A., Stumpel, Constance T.R.M., Tiller, George E., Bosch, Daniëlle G.M., Potgieter, Stephanus T., Joss, Shelagh, Splitt, Miranda, Holden, Simon, Prapa, Matina, Foulds, Nicola, Douzgou, Sofia, Puura, Kaija, Waltes, Regina, Chiocchetti, Andreas G., Freitag, Christine M., Satterstrom, F. Kyle, De Rubeis, Silvia, Buxbaum, Joseph, Gelb, Bruce D., Branko, Aleksic, Kushima, Itaru, Howe, Jennifer, Scherer, Stephen W., Arado, Alessia, Baldo, Chiara, Patat, Olivier, Bénédicte, Demeer, Lopergolo, Diego, Santorelli, Filippo M., Haack, Tobias B., Dufke, Andreas, Bertrand, Miriam, Falb, Ruth J., Rieß, Angelika, Krieg, Peter, Spranger, Stephanie, Bedeschi, Maria Francesca, Iascone, Maria, Josephi-Taylor, Sarah, Roscioli, Tony, Buckley, Michael F., Liebelt, Jan, Dagli, Aditi I., Aten, Emmelien, Hurst, Anna C.E., Hicks, Alesha, Suri, Mohnish, Aliu, Ermal, Naik, Sunil, Sidlow, Richard, Coursimault, Juliette, Nicolas, Gaël, Küpper, Hanna, Petit, Florence, Ibrahim, Veyan, Top, Deniz, Di Cara, Francesca, Louie, Raymond J., Stolerman, Elliot, Brunner, Han G., Vissers, Lisenka E.L.M., Kramer, Jamie M., and Kleefstra, Tjitske

Published
2023
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5. Genetic Alterations in Patients with NF2 -Related Schwannomatosis and Sporadic Vestibular Schwannomas.

Author

Douwes, Jules P. J., van Eijk, Ronald, Maas, Sybren L. N., Jansen, Jeroen C., Aten, Emmelien, and Hensen, Erik F.

Abstract

Simple Summary: Vestibular schwannomas are tumors that occur on the nerve responsible for hearing and balance, the vestibulocochlear nerve. These benign tumors may appear on one side (unilateral) or both sides (bilateral), with bilateral cases often linked to a condition called NF2-related schwannomatosis. This study explored the genetic causes of vestibular schwannomas in three groups: patients with NF2, younger patients with a unilateral tumor, and older patients with a unilateral tumor. By analyzing DNA from the tumors and blood, we aimed to understand the genetic mutations that drive tumor development and how the genetics differed between the three groups. In all patients, it was found that one gene, NF2, played a major role in the development of vestibular schwannomas. However, there were also differences found in the types of genetic mutations and mechanisms involved, offering new insights into how these tumors form and progress. Background: Unilateral (uVS) and bilateral vestibular schwannoma (bVS) are distinct disease types, yet share tumorigenic features. This study examined causative genetic alterations in three groups: patients with NF2-related schwannomatosis (NF2), young patients with uVS (≤30 years), and older patients with uVS (≥40 years). Methods: Lymphocyte and vestibular schwannoma DNA was genetically analyzed. Outcomes included gene involvement, pathogenicity classification, variant type, effect, and location, and loss of heterozygosity (LOH) of chromosome 22. Results: Among 93 patients, 17% had NF2, 39% were ≤30 years with uVS, and 44% were ≥40 years with uVS. In all patients with NF2 (100%), two or more hits were detected in the tumor DNA, whereas patients with uVS had a slightly lower detection rate (89–98%). NF2-related tumors had a higher frequency of nucleotide variants (76%), while LOH events were more common in uVS (64–69%). Variants were mostly identified in NF2, with nonsense variants over-represented in patients with NF2 (38%) and frameshift variants more prevalent in uVS (44–51%). Conclusions: Biallelic NF2 inactivation primarily drives vestibular schwannoma tumorigenesis. In patients with NF2, two pathogenic NF2 variants or one NF2 variant with LOH are common, whereas patients with uVS often exhibit one NF2 variant with LOH. Additionally, variant types differ between patient groups. [ABSTRACT FROM AUTHOR]

Published
2025
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6. Targeted sequencing identifies 91 neurodevelopmental-disorder risk genes with autism and developmental-disability biases

Author

Stessman, Holly AF, Xiong, Bo, Coe, Bradley P, Wang, Tianyun, Hoekzema, Kendra, Fenckova, Michaela, Kvarnung, Malin, Gerdts, Jennifer, Trinh, Sandy, Cosemans, Nele, Vives, Laura, Lin, Janice, Turner, Tychele N, Santen, Gijs, Ruivenkamp, Claudia, Kriek, Marjolein, van Haeringen, Arie, Aten, Emmelien, Friend, Kathryn, Liebelt, Jan, Barnett, Christopher, Haan, Eric, Shaw, Marie, Gecz, Jozef, Anderlid, Britt-Marie, Nordgren, Ann, Lindstrand, Anna, Schwartz, Charles, Kooy, R Frank, Vandeweyer, Geert, Helsmoortel, Celine, Romano, Corrado, Alberti, Antonino, Vinci, Mirella, Avola, Emanuela, Giusto, Stefania, Courchesne, Eric, Pramparo, Tiziano, Pierce, Karen, Nalabolu, Srinivasa, Amaral, David G, Scheffer, Ingrid E, Delatycki, Martin B, Lockhart, Paul J, Hormozdiari, Fereydoun, Harich, Benjamin, Castells-Nobau, Anna, Xia, Kun, Peeters, Hilde, Nordenskjöld, Magnus, Schenck, Annette, Bernier, Raphael A, and Eichler, Evan E

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Brain Disorders, Intellectual and Developmental Disabilities (IDD), Pediatric, Autism, Mental Health, Genetic Testing, Mental health, Autistic Disorder, Developmental Disabilities, Female, Humans, Intellectual Disability, Male, Mutation, Phenotype, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
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

10. Putting genome-wide sequencing in neonates into perspective

Author

van der Sluijs, Pleuntje J., Aten, Emmelien, Barge-Schaapveld, Daniela Q.C.M., Bijlsma, Emilia K., Bökenkamp-Gramann, Regina, Donker Kaat, Laura, van Doorn, Remco, van de Putte, Dietje Fransen, van Haeringen, Arie, ten Harkel, Arend D.J., Hilhorst-Hofstee, Yvonne, Hoffer, Mariette J.V., den Hollander, Nicolette S., van Ierland, Yvette, Koopmans, Marije, Kriek, Marjolein, Moghadasi, Setareh, Nibbeling, Esther A.R., Peeters-Scholte, Cacha M.P.C.D., Potjer, Thomas P., van Rij, Maartje, Ruivenkamp, Claudia A.L., Rutten, Julie W., Steggerda, Sylke J., Suerink, Manon, Tan, Ratna N.G.B., van der Tuin, Karin, Visser, Remco, van der Werf -'t Lam, Anne-Sophie, Williams, Monique, Witlox, Ruben, and Santen, Gijs W.E.

Published
2019
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11. Correction: Putting genome-wide sequencing in neonates into perspective

Author

van der Sluijs, Pleuntje J., Aten, Emmelien, Barge-Schaapveld, Daniela Q. C. M., Bijlsma, Emilia K., Bökenkamp-Gramann, Regina, Kaat, Laura Donker, van Doorn, Remco, van de Putte, Dietje Fransen, van Haeringen, Arie, ten Harkel, Arend D. J., Hilhorst-Hofstee, Yvonne, Hoffer, Mariette J. V., den Hollander, Nicolette S., van Ierland, Yvette, Koopmans, Marije, Kriek, Marjolein, Moghadasi, Setareh, Nibbeling, Esther A. R., Peeters-Scholte, Cacha M. P. C. D., Potjer, Thomas P., van Rij, Maartje, Ruivenkamp, Claudia A. L., Rutten, Julie W., Steggerda, Sylke J., Suerink, Manon, Tan, Ratna N. G. B., van der Tuin, Karin, Visser, Remco, van der Werf –’t Lam, Anne-Sophie, Williams, Monique, Witlox, Ruben, and Santen, Gijs W. E.

Published
2019
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12. The phenotypic spectrum of Schaaf-Yang syndrome: 18 new affected individuals from 14 families

Author

Fountain, Michael D., Aten, Emmelien, Cho, Megan T., Juusola, Jane, Walkiewicz, Magdalena A., Ray, Joseph W., Xia, Fan, Yang, Yaping, Graham, Brett H., Bacino, Carlos A., Potocki, Lorraine, van Haeringen, Arie, Ruivenkamp, Claudia A.L., Mancias, Pedro, Northrup, Hope, Kukolich, Mary K., Weiss, Marjan M., van Ravenswaaij-Arts, Conny M.A., Mathijssen, Inge B., Levesque, Sebastien, Meeks, Naomi, Rosenfeld, Jill A., Lemke, Danielle, Hamosh, Ada, Lewis, Suzanne K., Race, Simone, Stewart, Laura L., Hay, Beverly, Lewis, Andrea M., Guerreiro, Rita L., Bras, Jose T., Martins, Marcia P., Derksen-Lubsen, Gerarda, Peeters, Els, Stumpel, Connie, Stegmann, Sander, Bok, Levinus A., Santen, Gijs W.E., and Schaaf, Christian P.

Published
2017
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13. Consensus recommendations on organization of care for individuals with Phelan-McDermid syndrome

Author

van Eeghen, A. M., Gaasterland, C. M.W., Haneveld, M. J.Klein, Stemkens, D., Fernández-Fructuoso, José Ramón, Maruani, Anna, Hadzsiev, K., Hadzsiev, Kinga, van Balkom, Ingrid D.C., Alhambra, Norma, Anderlid, Britt Marie, Andres, Stephanie, Aten, Emmelien, Guedes, Rui Barbosa, Bonaglia, Maria C., Bourgeron, Thomas, Burdeus-Olavarrieta, Monica, Carbin, Maya J., Kuiper, Els, Cooke, Jennifer, Damstra, Robert J., de Coo, Irenaeus F.M., Di Domenico, Stella, Evans, D. Gareth, Grabrucker, Andreas M., Gunnarson, Cecilia, Hennekam, Raoul C., Jesse, Sarah, Kant, Sarina G., Koza, Sylvia A., van Ravenswaaij-Arts, Conny M.A., Walinga, Margreet, Landlust, Annemiek M., van Eeghen, A. M., Gaasterland, C. M.W., Haneveld, M. J.Klein, Stemkens, D., Fernández-Fructuoso, José Ramón, Maruani, Anna, Hadzsiev, K., Hadzsiev, Kinga, van Balkom, Ingrid D.C., Alhambra, Norma, Anderlid, Britt Marie, Andres, Stephanie, Aten, Emmelien, Guedes, Rui Barbosa, Bonaglia, Maria C., Bourgeron, Thomas, Burdeus-Olavarrieta, Monica, Carbin, Maya J., Kuiper, Els, Cooke, Jennifer, Damstra, Robert J., de Coo, Irenaeus F.M., Di Domenico, Stella, Evans, D. Gareth, Grabrucker, Andreas M., Gunnarson, Cecilia, Hennekam, Raoul C., Jesse, Sarah, Kant, Sarina G., Koza, Sylvia A., van Ravenswaaij-Arts, Conny M.A., Walinga, Margreet, and Landlust, Annemiek M.

Abstract

The manifestations of Phelan-McDermid syndrome (PMS) are complex, warranting expert and multidisciplinary care in all life stages. In the present paper we propose consensus recommendations on the organization of care for individuals with PMS. We indicate that care should consider all life domains, which can be done within the framework of the International Classification of Functioning, Disability and Health (ICF). This framework assesses disability and functioning as the outcome of the individual's interactions with other factors. The different roles within care, such as performed by a centre of expertise, by regional health care providers and by a coordinating physician are addressed. A surveillance scheme and emergency card is provided and disciplines participating in a multidisciplinary team for PMS are described. Additionally, recommendations are provided for transition from paediatric to adult care. This care proposition may also be useful for individuals with other rare genetic neurodevelopmental disorders.

Published
2023

14. High‐yield identification of pathogenic NF1 variants by skin fibroblast transcriptome screening after apparently normal diagnostic DNA testing

Author

Douben, Hannie C. W., primary, Nellist, Mark, additional, van Unen, Leontine, additional, Elfferich, Peter, additional, Kasteleijn, Esmee, additional, Hoogeveen‐Westerveld, Marianne, additional, Louwen, Jesse, additional, van Veghel‐Plandsoen, Monique, additional, de Valk, Walter, additional, Saris, Jasper J., additional, Hendriks, Femke, additional, Korpershoek, Esther, additional, Hoefsloot, Lies H., additional, van Vliet, Margreethe, additional, van Bever, Yolande, additional, van de Laar, Ingrid, additional, Aten, Emmelien, additional, Lachmeijer, Augusta M. A., additional, Taal, Walter, additional, van den Bersselaar, Lisa, additional, Schuurmans, Juliette, additional, Oostenbrink, Rianne, additional, van Minkelen, Rick, additional, van Ierland, Yvette, additional, and van Ham, Tjakko J., additional

Published
2022
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15. High-yield identification of pathogenic NF1 variants by skin fibroblast transcriptome screening after apparently normal diagnostic DNA testing

Author

Douben, Hannie C.W., Nellist, Mark, van Unen, Leontine, Elfferich, Peter, Kasteleijn, Esmee, Hoogeveen-Westerveld, Marianne, Louwen, Jesse, van Veghel-Plandsoen, Monique, de Valk, Walter, Saris, Jasper J., Hendriks, Femke, Korpershoek, Esther, Hoefsloot, Lies H., van Vliet, Margreethe, van Bever, Yolande, van de Laar, Ingrid, Aten, Emmelien, Lachmeijer, Augusta M.A., Taal, Walter, van den Bersselaar, Lisa, Schuurmans, Juliette, Oostenbrink, Rianne, van Minkelen, Rick, van Ierland, Yvette, van Ham, Tjakko J., Douben, Hannie C.W., Nellist, Mark, van Unen, Leontine, Elfferich, Peter, Kasteleijn, Esmee, Hoogeveen-Westerveld, Marianne, Louwen, Jesse, van Veghel-Plandsoen, Monique, de Valk, Walter, Saris, Jasper J., Hendriks, Femke, Korpershoek, Esther, Hoefsloot, Lies H., van Vliet, Margreethe, van Bever, Yolande, van de Laar, Ingrid, Aten, Emmelien, Lachmeijer, Augusta M.A., Taal, Walter, van den Bersselaar, Lisa, Schuurmans, Juliette, Oostenbrink, Rianne, van Minkelen, Rick, van Ierland, Yvette, and van Ham, Tjakko J.

Abstract

Neurofibromatosis type 1 (NF1) is caused by inactivating mutations in NF1. Due to the size, complexity, and high mutation rate at the NF1 locus, the identification of causative variants can be challenging. To obtain a molecular diagnosis in 15 individuals meeting diagnostic criteria for NF1, we performed transcriptome analysis (RNA-seq) on RNA obtained from cultured skin fibroblasts. In each case, routine molecular DNA diagnostics had failed to identify a disease-causing variant in NF1. A pathogenic variant or abnormal mRNA splicing was identified in 13 cases: 6 deep intronic variants and 2 transposon insertions causing noncanonical splicing, 3 postzygotic changes, 1 branch point mutation and, in 1 case, abnormal splicing for which the responsible DNA change remains to be identified. These findings helped resolve the molecular findings for an additional 17 individuals in multiple families with NF1, demonstrating the utility of skin-fibroblast-based transcriptome analysis for molecular diagnostics. RNA-seq improves mutation detection in NF1 and provides a powerful complementary approach to DNA-based methods. Importantly, our approach is applicable to other genetic disorders, particularly those caused by a wide variety of variants in a limited number of genes and specifically for individuals in whom routine molecular DNA diagnostics did not identify the causative variant.

Published
2022

16. Haploinsufficiency of the Sin3/HDAC corepressor complex member SIN3B causes a syndromic intellectual disability/autism spectrum disorder

Author

Latypova, Xenia, Vincent, Marie, Mollé, Alice, Adebambo, Oluwadamilare A., Fourgeux, Cynthia, Khan, Tahir N., Caro, Alfonso, Rosello, Monica, Orellana, Carmen, Niyazov, Dmitriy, Lederer, Damien, Deprez, Marie, Capri, Yline, Kannu, Peter, Tabet, Anne Claude, Levy, Jonathan, Aten, Emmelien, den Hollander, Nicolette, Splitt, Miranda, Walia, Jagdeep, Immken, Ladonna L., Stankiewicz, Pawel, McWalter, Kirsty, Suchy, Sharon, Louie, Raymond J., Bell, Shannon, Stevenson, Roger E., Rousseau, Justine, Willem, Catherine, Retiere, Christelle, Yang, Xiang-Jiao, Campeau, Philippe M., Martinez, Francisco, Rosenfeld, Jill A., Le Caignec, Cédric, Küry, Sébastien, Mercier, Sandra, Moradkhani, Kamran, Conrad, Solène, Besnard, Thomas, Cogné, Benjamin, Katsanis, Nicholas, Bézieau, Stéphane, Poschmann, Jeremie, Davis, Erica E., and Isidor, Bertrand

Published
2021
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17. Terminal osseous dysplasia is caused by a single recurrent mutation in the FLNA gene

Author

Yu Sun, Almomani, Rowida, Aten, Emmelien, Celli, Jacopo, Heijden, Jaap van der, Venselaar, Hanka, Robertson, Stephen P., Baroncini, Anna, Franco, Brunella, Basel-Vanagaite, Lina, Horii, Emiko, Drut, Ricardo, Ariyurek, Yavuz, Dunnen, Johan T. den, and Breuning, Martijn H.

Subjects
Dwarfism -- Genetic aspects, Gene expression -- Analysis, Gene mutations -- Analysis, Nucleotides -- Research, Biological sciences
Abstract

X-exome capture and sequencing was performed to identify a mutation at the last nucleotide of exon 31 of the FLNA gene as the most likely cause of the terminal osseous dysplasia (TOD) disease which is an x-linked dominant male-lethal disease characterized by skeletal dysplasia of the limbs, pigmentary defects of the skin and recurrent digital fibroma with onset in female infancy. The data obtained revealed that TOD is caused by single recurrent mutation in the FLNA gene.

Published
2010

18. Coffin–Siris Syndrome and the BAF Complex: Genotype–Phenotype Study in 63 Patients

Author

Santen, Gijs W.E., Aten, Emmelien, Vulto-van Silfhout, Anneke T., Pottinger, Caroline, van Bon, Bregje W.M., van Minderhout, Ivonne J.H.M., Snowdowne, Ronelle, van der Lans, Christian A.C., Boogaard, Merel, Linssen, Margot M.L., Vijfhuizen, Linda, van der Wielen, Michiel J.R., Vollebregt, M. J. (Ellen), Breuning, Martijn H., Kriek, Marjolein, van Haeringen, Arie, den Dunnen, Johan T., Hoischen, Alexander, Clayton-Smith, Jill, de Vries, Bert B.A., Hennekam, Raoul C.M., and van Belzen, Martine J.

Published
2013
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20. Autosomal Recessive Spinocerebellar Ataxia 7 (SCAR7) is Caused by Variants in TPP1, The Gene Involved in Classic Late-Infantile Neuronal Ceroid Lipofuscinosis 2 Disease (CLN2 Disease)

Author

Sun, Yu, Almomani, Rowida, Breedveld, Guido J., Santen, Gijs W.E., Aten, Emmelien, Lefeber, Dirk J., Hoff, Jorrit I., Brusse, Esther, Verheijen, Frans W., Verdijk, Rob M., Kriek, Marjolein, Oostra, Ben, Breuning, Martijn H., Losekoot, Monique, den Dunnen, Johan T., van de Warrenburg, Bart P., and Maat-Kievit, Anneke J.A.

Published
2013
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24. Identification of known and unknown genes associated with mitral valve prolapse using an exome slice methodology

Author

van Wijngaarden, Aniek L, primary, Hiemstra, Yasmine L, additional, Koopmann, Tamara T, additional, Ruivenkamp, Claudia A L, additional, Aten, Emmelien, additional, Schalij, Martin J, additional, Bax, Jeroen J, additional, Delgado, Victoria, additional, Barge-Schaapveld, Daniela Q C M, additional, and Ajmone Marsan, Nina, additional

Published
2020
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29. Correction: Putting genome-wide sequencing in neonates into perspective

Author

Genetica Klinische Genetica, Cancer, van der Sluijs, Pleuntje J., Aten, Emmelien, Barge-Schaapveld, Daniela Q.C.M., Bijlsma, Emilia K., Bökenkamp-Gramann, Regina, Kaat, Laura Donker, van Doorn, Remco, van de Putte, Dietje Fransen, van Haeringen, Arie, ten Harkel, Arend D.J., Hilhorst-Hofstee, Yvonne, Hoffer, Mariette J.V., den Hollander, Nicolette S., van Ierland, Yvette, Koopmans, Marije, Kriek, Marjolein, Moghadasi, Setareh, Nibbeling, Esther A.R., Peeters-Scholte, Cacha M.P.C.D., Potjer, Thomas P., van Rij, Maartje, Ruivenkamp, Claudia A.L., Rutten, Julie W., Steggerda, Sylke J., Suerink, Manon, Tan, Ratna N.G.B., van der Tuin, Karin, Visser, Remco, van der Werf–t Lam, Anne Sophie, Williams, Monique, Witlox, Ruben, Santen, Gijs W.E., Genetica Klinische Genetica, Cancer, van der Sluijs, Pleuntje J., Aten, Emmelien, Barge-Schaapveld, Daniela Q.C.M., Bijlsma, Emilia K., Bökenkamp-Gramann, Regina, Kaat, Laura Donker, van Doorn, Remco, van de Putte, Dietje Fransen, van Haeringen, Arie, ten Harkel, Arend D.J., Hilhorst-Hofstee, Yvonne, Hoffer, Mariette J.V., den Hollander, Nicolette S., van Ierland, Yvette, Koopmans, Marije, Kriek, Marjolein, Moghadasi, Setareh, Nibbeling, Esther A.R., Peeters-Scholte, Cacha M.P.C.D., Potjer, Thomas P., van Rij, Maartje, Ruivenkamp, Claudia A.L., Rutten, Julie W., Steggerda, Sylke J., Suerink, Manon, Tan, Ratna N.G.B., van der Tuin, Karin, Visser, Remco, van der Werf–t Lam, Anne Sophie, Williams, Monique, Witlox, Ruben, and Santen, Gijs W.E.

Published
2019

30. Genetic islands of Streptococcus agalactiae strains NEM316 and 2603VR and their presence in other Group B Streptococcal strains

Author

Snyder Lori AS, Jones Nicola, Aten Emmelien, McCormick David, Beveridge Catriona JE, Herbert Mark A, and Saunders Nigel J

Subjects
Microbiology, QR1-502
Abstract

Abstract Background Streptococcus agalactiae (Group B Streptococcus; GBS) is a major contributor to obstetric and neonatal bacterial sepsis. Serotype III strains cause the majority of late-onset sepsis and meningitis in babies, and thus appear to have an enhanced invasive capacity compared with the other serotypes that cause disease predominantly in immunocompromised pregnant women. We compared the serotype III and V whole genome sequences, strains NEM316 and 2603VR respectively, in an attempt to identify genetic attributes of strain NEM316 that might explain the propensity of strain NEM316 to cause late-onset disease in babies. Fourteen putative pathogenicity islands were described in the strain NEM316 whole genome sequence. Using PCR- and targeted microarray- strategies, the presence of these islands were assessed in a diverse strain collection including 18 colonizing isolates from healthy pregnant women, and 13 and 8 invasive isolates from infants with early- and late-onset sepsis, respectively. Results Side-by-side comparison of the strain NEM316 and strain 2603VR genomes revealed that they are extremely similar, with the only major difference being the capsulation loci and mobile genetic elements. PCR and Comparative Genome Hybridization (CGH) were used to define the presence of each island in 39 GBS isolates. Only islands I, VI, XII, and possibly X, met criteria of a true pathogenicity island, but no significant correlation was found between the presence of any of the fourteen islands and whether the strains were invasive or colonizing. Possible associations were seen between the presence of island VI and late-onset sepsis, and island X and early-onset sepsis, which warrant further investigation. Conclusion The NEM316 and 2603VR strains are remarkable in that their whole genome sequences are so similar, suggesting that the capsulation loci or other genetic differences, such as pathogenicity islands, are the main determinants of the propensity of serotype III strains to cause late-onset disease. This study supports the notion that GBS strain NEM316 has four putative pathogenicity islands, but none is absolutely necessary for disease causation, whether early- or late-onset sepsis. Mobile genetic elements are a common feature of GBS isolates, with each strain having its own peculiar burden of transposons, phages, integrases and integrated plasmids. The majority of these are unlikely to influence the disease capacity of an isolate. Serotype associated disease phenotypes may thus be solely related to differences in the capsulation loci.

Published
2005
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31. Lamin A/C -Related Cardiac Disease

Author

Hoorntje, Edgar T., primary, Bollen, Ilse A., additional, Barge-Schaapveld, Daniela Q., additional, van Tienen, Florence H., additional, te Meerman, Gerard J., additional, Jansweijer, Joeri A., additional, van Essen, Anthonie J., additional, Volders, Paul G., additional, Constantinescu, Alina A., additional, van den Akker, Peter C., additional, van Spaendonck-Zwarts, Karin Y., additional, Oldenburg, Rogier A., additional, Marcelis, Carlo L., additional, van der Smagt, Jasper J., additional, Hennekam, Eric A., additional, Vink, Aryan, additional, Bootsma, Marianne, additional, Aten, Emmelien, additional, Wilde, Arthur A., additional, van den Wijngaard, Arthur, additional, Broers, Jos L., additional, Jongbloed, Jan D., additional, van der Velden, Jolanda, additional, van den Berg, Maarten P., additional, and van Tintelen, J. Peter, additional

Published
2017
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32. Lamin A/C-Related Cardiac Disease : Late Onset With a Variable and Mild Phenotype in a Large Cohort of Patients With the Lamin A/C p.(Arg331Gln) Founder Mutation

Author

Hoorntje, Edgar T, Bollen, Ilse Ae, Barge-Schaapveld, Daniela Q, Van Tienen, Florence H J, Te Meerman, Gerard J, Jansweijer, Joeri A, van Essen, Anthonie J, Volders, Paul G. A., Constantinescu, Alina, Van Den Akker, Peter C., van Spaendonck-Zwarts, Karin Y., Oldenburg, Rogier A, Marcelis, Carlo L. M., van der Smagt, Jasper J, Hennekam, Eric A, Vink, Aryan, Bootsma, Marianne, Aten, Emmelien, Wilde, Arthur A A M, van den Wijngaard, Arthur, Broers, Jos L, Jongbloed, Jan D. H., van der Velden, Jolanda, van den Berg, Maarten P., van Tintelen, J. Peter, Hoorntje, Edgar T, Bollen, Ilse Ae, Barge-Schaapveld, Daniela Q, Van Tienen, Florence H J, Te Meerman, Gerard J, Jansweijer, Joeri A, van Essen, Anthonie J, Volders, Paul G. A., Constantinescu, Alina, Van Den Akker, Peter C., van Spaendonck-Zwarts, Karin Y., Oldenburg, Rogier A, Marcelis, Carlo L. M., van der Smagt, Jasper J, Hennekam, Eric A, Vink, Aryan, Bootsma, Marianne, Aten, Emmelien, Wilde, Arthur A A M, van den Wijngaard, Arthur, Broers, Jos L, Jongbloed, Jan D. H., van der Velden, Jolanda, van den Berg, Maarten P., and van Tintelen, J. Peter

Published
2017

33. Lamin A/C-Related Cardiac Disease: Late Onset With a Variable and Mild Phenotype in a Large Cohort of Patients With the Lamin A/C p.(Arg331Gln) Founder Mutation

Author

Genetica Klinische Genetica, Circulatory Health, Pathologie Pathologen staf, Hoorntje, Edgar T, Bollen, Ilse Ae, Barge-Schaapveld, Daniela Q, Van Tienen, Florence H J, Te Meerman, Gerard J, Jansweijer, Joeri A, van Essen, Anthonie J, Volders, Paul G. A., Constantinescu, Alina, Van Den Akker, Peter C., van Spaendonck-Zwarts, Karin Y., Oldenburg, Rogier A, Marcelis, Carlo L. M., van der Smagt, Jasper J, Hennekam, Eric A, Vink, Aryan, Bootsma, Marianne, Aten, Emmelien, Wilde, Arthur A A M, van den Wijngaard, Arthur, Broers, Jos L, Jongbloed, Jan D. H., van der Velden, Jolanda, van den Berg, Maarten P., van Tintelen, J. Peter, Genetica Klinische Genetica, Circulatory Health, Pathologie Pathologen staf, Hoorntje, Edgar T, Bollen, Ilse Ae, Barge-Schaapveld, Daniela Q, Van Tienen, Florence H J, Te Meerman, Gerard J, Jansweijer, Joeri A, van Essen, Anthonie J, Volders, Paul G. A., Constantinescu, Alina, Van Den Akker, Peter C., van Spaendonck-Zwarts, Karin Y., Oldenburg, Rogier A, Marcelis, Carlo L. M., van der Smagt, Jasper J, Hennekam, Eric A, Vink, Aryan, Bootsma, Marianne, Aten, Emmelien, Wilde, Arthur A A M, van den Wijngaard, Arthur, Broers, Jos L, Jongbloed, Jan D. H., van der Velden, Jolanda, van den Berg, Maarten P., and van Tintelen, J. Peter

Published
2017

35. The Implicitome: A Resource for Rationalizing Gene-Disease Associations

Author

Hettne, Kristina M., primary, Thompson, Mark, additional, van Haagen, Herman H. H. B. M., additional, van der Horst, Eelke, additional, Kaliyaperumal, Rajaram, additional, Mina, Eleni, additional, Tatum, Zuotian, additional, Laros, Jeroen F. J., additional, van Mulligen, Erik M., additional, Schuemie, Martijn, additional, Aten, Emmelien, additional, Li, Tong Shu, additional, Bruskiewich, Richard, additional, Good, Benjamin M., additional, Su, Andrew I., additional, Kors, Jan A., additional, den Dunnen, Johan, additional, van Ommen, Gert-Jan B., additional, Roos, Marco, additional, ‘t Hoen, Peter A.C., additional, Mons, Barend, additional, and Schultes, Erik A., additional

Published
2016
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37. Structural genomic variation in childhood epilepsies with complex phenotypes

Author

Helbig, Ingo, Swinkels, Marielle E M, Aten, Emmelien, Caliebe, Almuth, van 't Slot, Ruben, Boor, Rainer, von Spiczak, Sarah, Muhle, Hiltrud, Jähn, Johanna A, van Binsbergen, Ellen, van Nieuwenhuizen, Onno, Jansen, Floor E, Braun, Kees P J, de Haan, Gerrit-Jan, Tommerup, Niels, Stephani, Ulrich, Hjalgrim, Helle, Poot, Martin, Lindhout, Dick, Brilstra, Eva H, Møller, Rikke S, Koeleman, Bobby P C, Helbig, Ingo, Swinkels, Marielle E M, Aten, Emmelien, Caliebe, Almuth, van 't Slot, Ruben, Boor, Rainer, von Spiczak, Sarah, Muhle, Hiltrud, Jähn, Johanna A, van Binsbergen, Ellen, van Nieuwenhuizen, Onno, Jansen, Floor E, Braun, Kees P J, de Haan, Gerrit-Jan, Tommerup, Niels, Stephani, Ulrich, Hjalgrim, Helle, Poot, Martin, Lindhout, Dick, Brilstra, Eva H, Møller, Rikke S, and Koeleman, Bobby P C

Abstract

A genetic contribution to a broad range of epilepsies has been postulated, and particularly copy number variations (CNVs) have emerged as significant genetic risk factors. However, the role of CNVs in patients with epilepsies with complex phenotypes is not known. Therefore, we investigated the role of CNVs in patients with unclassified epilepsies and complex phenotypes. A total of 222 patients from three European countries, including patients with structural lesions on magnetic resonance imaging (MRI), dysmorphic features, and multiple congenital anomalies, were clinically evaluated and screened for CNVs. MRI findings including acquired or developmental lesions and patient characteristics were subdivided and analyzed in subgroups. MRI data were available for 88.3% of patients, of whom 41.6% had abnormal MRI findings. Eighty-eight rare CNVs were discovered in 71 out of 222 patients (31.9%). Segregation of all identified variants could be assessed in 42 patients, 11 of which were de novo. The frequency of all structural variants and de novo variants was not statistically different between patients with or without MRI abnormalities or MRI subcategories. Patients with dysmorphic features were more likely to carry a rare CNV. Genome-wide screening methods for rare CNVs may provide clues for the genetic etiology in patients with a broader range of epilepsies than previously anticipated, including in patients with various brain anomalies detectable by MRI. Performing genome-wide screens for rare CNVs can be a valuable contribution to the routine diagnostic workup in patients with a broad range of childhood epilepsies.

Published
2014

38. Structural genomic variation in childhood epilepsies with complex phenotypes

Author

Helbig, Ingo, primary, Swinkels, Marielle E M, additional, Aten, Emmelien, additional, Caliebe, Almuth, additional, van 't Slot, Ruben, additional, Boor, Rainer, additional, von Spiczak, Sarah, additional, Muhle, Hiltrud, additional, Jähn, Johanna A, additional, van Binsbergen, Ellen, additional, van Nieuwenhuizen, Onno, additional, Jansen, Floor E, additional, Braun, Kees P J, additional, de Haan, Gerrit-Jan, additional, Tommerup, Niels, additional, Stephani, Ulrich, additional, Hjalgrim, Helle, additional, Poot, Martin, additional, Lindhout, Dick, additional, Brilstra, Eva H, additional, Møller, Rikke S, additional, and Koeleman, Bobby PC, additional

Published
2013
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39. GPSM2and Chudley-McCullough Syndrome: A Dutch Founder Variant Brought to North America

Author

Almomani, Rowida, primary, Sun, Yu, additional, Aten, Emmelien, additional, Hilhorst-Hofstee, Yvonne, additional, Peeters-Scholte, Cacha M.P.C.D., additional, van Haeringen, Arie, additional, Hendriks, Yvonne M.C., additional, den Dunnen, Johan T., additional, Breuning, Martijn H., additional, Kriek, Marjolein, additional, and Santen, Gijs W.E., additional

Published
2013
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40. Autosomal Recessive Spinocerebellar Ataxia 7 (SCAR7) is Caused by Variants inTPP1, The Gene Involved in Classic Late-Infantile Neuronal Ceroid Lipofuscinosis 2 Disease (CLN2 Disease)

Author

Sun, Yu, primary, Almomani, Rowida, additional, Breedveld, Guido J., additional, Santen, Gijs W.E., additional, Aten, Emmelien, additional, Lefeber, Dirk J., additional, Hoff, Jorrit I., additional, Brusse, Esther, additional, Verheijen, Frans W., additional, Verdijk, Rob M., additional, Kriek, Marjolein, additional, Oostra, Ben, additional, Breuning, Martijn H., additional, Losekoot, Monique, additional, den Dunnen, Johan T., additional, van de Warrenburg, Bart P., additional, and Maat-Kievit, Anneke J.A., additional

Published
2013
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41. Mutations in SWI/SNF chromatin remodeling complex gene ARID1B cause Coffin-Siris syndrome

Author

Santen, Gijs W E, primary, Aten, Emmelien, additional, Sun, Yu, additional, Almomani, Rowida, additional, Gilissen, Christian, additional, Nielsen, Maartje, additional, Kant, Sarina G, additional, Snoeck, Irina N, additional, Peeters, Els A J, additional, Hilhorst-Hofstee, Yvonne, additional, Wessels, Marja W, additional, den Hollander, Nicolette S, additional, Ruivenkamp, Claudia A L, additional, van Ommen, Gert-Jan B, additional, Breuning, Martijn H, additional, den Dunnen, Johan T, additional, van Haeringen, Arie, additional, and Kriek, Marjolein, additional

Published
2012
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42. GPSM 2 and Chudley- Mc Cullough Syndrome: A Dutch Founder Variant Brought to North America.

Author

Almomani, Rowida, Sun, Yu, Aten, Emmelien, Hilhorst‐Hofstee, Yvonne, Peeters‐Scholte, Cacha M.P.C.D., van Haeringen, Arie, Hendriks, Yvonne M.C., den Dunnen, Johan T., Breuning, Martijn H., Kriek, Marjolein, and Santen, Gijs W.E.

Abstract

Chudley-McCullough syndrome (CMS) is characterized by profound sensorineural hearing loss and brain anomalies. Variants in GPSM2 have recently been reported as a cause of CMS by Doherty et al. In this study we have performed exome sequencing of three CMS patients from two unrelated families from the same Dutch village. We identified one homozygous frameshift GPSM2 variants c.1473delG in all patients. We show that this variant arises from a shared, rare haplotype. Since the c.1473delG variant was found in Mennonite settlers, it likely originated in Europe. To support DNA diagnostics, we established an LOVD database for GPSM2 containing all variants thus far described. © 2013 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Published
2013
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43. Genetic islands of Streptococcus agalactiae strains NEM316 and 2603VR and their presence in other Group B Streptococcal strains.

Author

Herbert, Mark A., Beveridge, Catriona J.E., McCormick, David, Aten, Emmelien, Jones, Nicola, Snyder, Lori A.S., and Saunders, Nigel J.

Subjects
STREPTOCOCCUS agalactiae, SEPSIS, MENINGITIS, PREGNANT women, GENOMES
Abstract

Background: Streptococcus agalactiae (Group B Streptococcus; GBS) is a major contributor to obstetric and neonatal bacterial sepsis. Serotype III strains cause the majority of late-onset sepsis and meningitis in babies, and thus appear to have an enhanced invasive capacity compared with the other serotypes that cause disease predominantly in immunocompromised pregnant women. We compared the serotype III and V whole genome sequences, strains NEM316 and 2603VR respectively, in an attempt to identify genetic attributes of strain NEM316 that might explain the propensity of strain NEM316 to cause late-onset disease in babies. Fourteen putative pathogenicity islands were described in the strain NEM316 whole genome sequence. Using PCR- and targeted microarray- strategies, the presence of these islands were assessed in a diverse strain collection including 18 colonizing isolates from healthy pregnant women, and 13 and 8 invasive isolates from infants with early- and late-onset sepsis, respectively. Results: Side-by-side comparison of the strain NEM316 and strain 2603VR genomes revealed that they are extremely similar, with the only major difference being the capsulation loci and mobile genetic elements. PCR and Comparative Genome Hybridization (CGH) were used to define the presence of each island in 39 GBS isolates. Only islands I, VI, XII, and possibly X, met criteria of a true pathogenicity island, but no significant correlation was found between the presence of any of the fourteen islands and whether the strains were invasive or colonizing. Possible associations were seen between the presence of island VI and late-onset sepsis, and island X and early-onset sepsis, which warrant further investigation. Conclusion: The NEM316 and 2603VR strains are remarkable in that their whole genome sequences are so similar, suggesting that the capsulation loci or other genetic differences, such as pathogenicity islands, are the main determinants of the propensity of serotype III strains to cause late-onset disease. This study supports the notion that GBS strain NEM316 has four putative pathogenicity islands, but none is absolutely necessary for disease causation, whether earlyor late-onset sepsis. Mobile genetic elements are a common feature of GBS isolates, with each strain having its own peculiar burden of transposons, phages, integrases and integrated plasmids. The majority of these are unlikely to influence the disease capacity of an isolate. Serotype associated disease phenotypes may thus be solely related to differences in the capsulation loci. [ABSTRACT FROM AUTHOR]

Published
2005
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44. Structural genomic variation in childhood epilepsies with complex phenotypes.

Author

Helbig I, Swinkels ME, Aten E, Caliebe A, van 't Slot R, Boor R, von Spiczak S, Muhle H, Jähn JA, van Binsbergen E, van Nieuwenhuizen O, Jansen FE, Braun KP, de Haan GJ, Tommerup N, Stephani U, Hjalgrim H, Poot M, Lindhout D, Brilstra EH, Møller RS, and Koeleman BP

Subjects
Adolescent, Adult, Child, Preschool, Female, Genome-Wide Association Study, Humans, Infant, Male, Radiography, Abnormalities, Multiple diagnostic imaging, Abnormalities, Multiple genetics, Epilepsy diagnostic imaging, Epilepsy genetics, Gene Dosage, Genetic Variation, Magnetic Resonance Imaging, Phenotype
Abstract

A genetic contribution to a broad range of epilepsies has been postulated, and particularly copy number variations (CNVs) have emerged as significant genetic risk factors. However, the role of CNVs in patients with epilepsies with complex phenotypes is not known. Therefore, we investigated the role of CNVs in patients with unclassified epilepsies and complex phenotypes. A total of 222 patients from three European countries, including patients with structural lesions on magnetic resonance imaging (MRI), dysmorphic features, and multiple congenital anomalies, were clinically evaluated and screened for CNVs. MRI findings including acquired or developmental lesions and patient characteristics were subdivided and analyzed in subgroups. MRI data were available for 88.3% of patients, of whom 41.6% had abnormal MRI findings. Eighty-eight rare CNVs were discovered in 71 out of 222 patients (31.9%). Segregation of all identified variants could be assessed in 42 patients, 11 of which were de novo. The frequency of all structural variants and de novo variants was not statistically different between patients with or without MRI abnormalities or MRI subcategories. Patients with dysmorphic features were more likely to carry a rare CNV. Genome-wide screening methods for rare CNVs may provide clues for the genetic etiology in patients with a broader range of epilepsies than previously anticipated, including in patients with various brain anomalies detectable by MRI. Performing genome-wide screens for rare CNVs can be a valuable contribution to the routine diagnostic workup in patients with a broad range of childhood epilepsies.

Published
2014
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