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1. Rapid whole exome sequencing in pregnancies to identify the underlying genetic cause in fetuses with congenital anomalies detected by ultrasound imaging

Author

Deden, C. (Chantal), Neveling, K. (Kornelia), Zafeiropopoulou, D. (Dimitra), Gilissen, C. (Christian), Pfundt, R. (Rolph), Rinne, T. (Tuula), Leeuw, N. (Nicole) de, Faas, B.H.W. (Brigitte), Gardeitchik, T. (Thatjana), Sallevelt, S.C.E.H. (Suzanne), Paulussen, A.D.C. (Aimée), Stevens, S.J.C. (Servi J. C.), Sikkel, E. (Esther), Elting, M. (Mariet), Maarle, M.C. (Merel), Diderich, K.E.M. (Karin), Corsten-Janssen, N. (Nicole), Lichtenbelt, K.D. (Klaske), Lachmeijer, G. (Guus), Vissers, L.E.L.M., Yntema, H.G., Nelen, M. (Marcel), Feenstra, I. (Ilse), Zelst-Stams, W.A. van, Deden, C. (Chantal), Neveling, K. (Kornelia), Zafeiropopoulou, D. (Dimitra), Gilissen, C. (Christian), Pfundt, R. (Rolph), Rinne, T. (Tuula), Leeuw, N. (Nicole) de, Faas, B.H.W. (Brigitte), Gardeitchik, T. (Thatjana), Sallevelt, S.C.E.H. (Suzanne), Paulussen, A.D.C. (Aimée), Stevens, S.J.C. (Servi J. C.), Sikkel, E. (Esther), Elting, M. (Mariet), Maarle, M.C. (Merel), Diderich, K.E.M. (Karin), Corsten-Janssen, N. (Nicole), Lichtenbelt, K.D. (Klaske), Lachmeijer, G. (Guus), Vissers, L.E.L.M., Yntema, H.G., Nelen, M. (Marcel), Feenstra, I. (Ilse), and Zelst-Stams, W.A. van

Abstract

Objective: The purpose of this study was to explore the diagnostic yield and clinical utility of trio-based rapid whole exome sequencing (rWES) in pregnancies of fetuses with a wide range of congenital anomalies detected by ultrasound imaging. Methods: In this observational study, we analyzed the first 54 cases referred to our laboratory for prenatal rWES to support clinical decision making, after the sonographic detection of fetal congenital anomalies. The most common identified congenital anomalies were skeletal dysplasia (n = 20), multiple major fetal congenital anomalies (n = 17) and intracerebral structural anomalies (n = 7). Results: A conclusive diagnosis was identified in 18 of the 54 cases (33%). Pathogenic variants were detected most often in fetuses with skeletal dysplasia (n = 11) followed by fetuses with multiple major fetal congenital anomalies (n = 4) and intracerebral structural anomalies (n = 3). A survey, completed by the physicians for 37 of 54 cases, indicated that the rWES results impacted clinical decision making in 68% of cases. Conclusions: These results suggest that rWES improves prenatal diagnosis of fetuses with congenital anomalies, and has an important impact on prenatal and peripartum parental and clinical decision making.

Published
2020
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2. PRRT2-related phenotypes in patients with a 16p11.2 deletion

Author

Vlaskamp, D.R.M. (Danique R.M.), Callenbach, P.M.C. (Petra), Rump, P. (Patrick), Giannini, L.A.A. (Lucia A.A.), Brilstra, E.H. (Eva H.), Dijkhuizen, T. (Trijnie), Vos, Y.J. (Yvonne), van der Kevie-Kersemaekers, A.M.F., Knijnenburg, J. (Jeroen), Leeuw, N. (Nicole) de, Thornton, A.S. (Andrew), Ruivenkamp, C.A. (Claudia), Stegmann, A.P.A. (Alexander P.A.), Brouwer, O.F. (Oebele), Ravenswaaij-Arts, C.M.A. (Conny) van, Vlaskamp, D.R.M. (Danique R.M.), Callenbach, P.M.C. (Petra), Rump, P. (Patrick), Giannini, L.A.A. (Lucia A.A.), Brilstra, E.H. (Eva H.), Dijkhuizen, T. (Trijnie), Vos, Y.J. (Yvonne), van der Kevie-Kersemaekers, A.M.F., Knijnenburg, J. (Jeroen), Leeuw, N. (Nicole) de, Thornton, A.S. (Andrew), Ruivenkamp, C.A. (Claudia), Stegmann, A.P.A. (Alexander P.A.), Brouwer, O.F. (Oebele), and Ravenswaaij-Arts, C.M.A. (Conny) van

Abstract

We studied the presence of benign infantile epilepsy (BIE), paroxysmal kinesigenic dyskinesia (PKD), and PKD with infantile convulsions (PKD/IC) in patients with a 16p11.2 deletion including PRRT2 or with a PRRT2 loss-of-function sequence variant. Index patients were recruited from seven Dutch university hospitals. The presence of BIE, PKD and PKD/IC was retrospectively evaluated using questionnaires and medical records. We included 33 patients with a 16p11.2 deletion: three (9%) had BIE, none had PKD or PKD/IC. Twelve patients had a PRRT2 sequence variant: BIE was present in four (p = 0.069), PKD in six (p < 0.001) and PKD/IC in two (p = 0.067). Most patients with a deletion had undergone genetic testing because of developmental problems (87%), whereas all patients with a sequence variant were tested because of a movement disorder (55%) or epilepsy (45%). BIE, PKD and PKD/IC clearly showed incomplete penetrance in patients with 16p11.2 deletions, but were found in all and 95% of patients with a PRRT2 sequence variant in our study and a large literature cohort, respectively. Deletions and sequence variants have the same underlying loss-of-function disease mechanism. Thus, differences in ascertainment have led to overestimating the frequency of BIE, PKD and PKD/IC in patients with a PRRT2 sequence variant. This has important implications for counseling if genome-wide sequencing shows such variants in patients not presenting the PRRT2-related phenotypes.

Published
2018
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3. The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies

Author

Redin, C. (Claire), Brand, H. (Harrison), Collins, R.L. (Ryan L.), Kammin, T. (Tammy), Mitchell, E. (Elyse), Hodge, J.C. (Jennelle C.), Hanscom, C. (Carrie), Pillalamarri, V. (Vamsee), Seabra, C.M. (Catarina M.), Abbott, M.-A. (Mary-Alice), Abdul-Rahman, O.A. (Omar), Aberg, E. (Erika), Adley, R. (Rhett), Alcaraz-Estrada, S.L. (Sofia L.), Alkuraya, F.S. (Fowzan S), An, Y. (Yu), Anderson, M.-A. (Mary-Anne), Antolik, C. (Caroline), Anyane-Yeboa, K. (Kwame), Atkin, J.F. (Joan), Bartell, T. (Tina), Bernstein, J.A. (Jonathan A.), Beyer, E. (Elizabeth), Blumenthal, I. (Ian), Bongers, E. (Ernie), Brilstra, E.H. (Eva H.), Brown, C.W. (Chester W.), Brüggenwirth, H.T. (Hennie), Callewaert, L., Chiang, C. (Colby), Corning, K. (Ken), Cox, H. (H.), Cuppen, E. (Edwin), Currall, B.B. (Benjamin B.), Cushing, T. (Tom), David, D. (Dezso), Deardorff, M.A. (Matthew), Dheedene, A. (Annelies), D'Hooghe, M. (Marc), Vries, B. (Boukje) de, Earl, D.L. (Dawn L.), Ferguson, H.L. (Heather L.), Fisher, H. (Heather), Fitzpatrick, D.R. (David R.), Gerrol, P. (Pamela), Giachino, D. (Daniela), Glessner, J.T. (Joseph T.), Gliem, T. (Troy), Grady, M. (Margo), Graham, B.H. (Brett H.), Griffis, C. (Cristin), Gripp, K.W. (Karen), Gropman, A.L. (Andrea L.), Hanson-Kahn, A. (Andrea), Harris, D.J. (David J.), Hayden, M.A. (Mark A.), Hill, R. (Rosamund), Hochstenbach, R. (Ron), Hoffman, J.D. (Jodi D.), Hopkin, R., Hubshman, M.W. (Monika W.), Innes, M., Irons, M. (Mira), Irving, M. (Melita), Jacobsen, J.C. (Jessie C.), Janssens, S. (Sandra), Jewett, T. (Tamison), Johnson, J.P. (John P.), Jongmans, M.C.J. (Marjolijn), Kahler, S.G. (Stephen G.), Koolen, D.A. (David), Korzelius, J. (Jerome), Kroisel, P. (Peter), Lacassie, Y. (Yves), Lawless, W. (William), Lemyre, E. (Emmanuelle), Leppig, K. (Kathy), Levin, A.V. (Alex V.), Li, H. (Haibo), Li, H. (Hong), Liao, E.C. (Eric C.), Lim, C. (Cynthia), Lose, E.J. (Edward J.), Lucente, D. (Diane), MacEra, M.J. (Michael J.), Manavalan, P. (Poornima), Mandrile, G. (Giorgia), Marcelis, C.L.M. (Carlo), Margolin, L. (Lauren), Mason, T. (Tamara), Masser-Frye, D. (Diane), McClellan, M.W. (Michael W.), Zepeda Mendoza, C.J. (Cinthya J.), Menten, B., Middelkamp, S. (Sjors), Mikami, L.R. (Liya R.), Moe, E. (Emily), Mohammed, S. (Shabaz), Mononen, T. (Tarja), Mortenson, M.E. (Megan E.), Moya, G. (Graciela), Nieuwint, A.W. (Aggie W.), Ordulu, Z. (Zehra), Parkash, S. (Sandhya), Pauker, S.P. (Susan P.), Pereira, S. (Shahrin), Perrin, D. (Danielle), Phelan, K. (Katy), Piña Aguilar, R.E. (Raul E.), Poddighe, P. (Pino), Pregno, G. (Giulia), Raskin, S. (Salmo), Reis, L. (Linda), Rhead, W. (William), Rita, D. (Debra), Renkens, I. (Ivo), Roelens, F. (Filip), Ruliera, J. (Jayla), Rump, P. (Patrick), Schilit, S.L.P. (Samantha L.P.), Shaheen, R. (Ranad), Sparkes, R. (Rebecca), Spiegel, E. (Erica), Stevens, B. (Blair), Stone, M.R. (Matthew R.), Tagoe, J. (Julia), Thakuria, J.V. (Joseph V.), Bon, B. (Bregje) van, van de Kamp, J.M. (Jiddeke M.), Van Der Burgt, I. (Ineke), Essen, T. (Ton) van, Ravenswaaij-Arts, C.M.A. (Conny) van, Van Roosmalen, M.J. (Markus J.), Vergult, S. (Sarah), Volker-Touw, C.M.L. (Catharina M.L.), Warburton, D. (Dorothy), Waterman, M.J. (Matthew J.), Wiley, S. (Susan), Wilson, A. (Anna), Yerena-De Vega, M.D.L.C.A. (Maria De La Concepcion A), Zori, R.T. (Roberto T.), Levy, B. (Brynn), Brunner, H.G. (Han), Leeuw, N. (Nicole) de, Kloosterman, W.P. (Wigard), Thorland, E.C. (Erik C.), Morton, C.C. (Cynthia), Gusella, J.F. (James), Talkowski, M.E. (Michael E.), Redin, C. (Claire), Brand, H. (Harrison), Collins, R.L. (Ryan L.), Kammin, T. (Tammy), Mitchell, E. (Elyse), Hodge, J.C. (Jennelle C.), Hanscom, C. (Carrie), Pillalamarri, V. (Vamsee), Seabra, C.M. (Catarina M.), Abbott, M.-A. (Mary-Alice), Abdul-Rahman, O.A. (Omar), Aberg, E. (Erika), Adley, R. (Rhett), Alcaraz-Estrada, S.L. (Sofia L.), Alkuraya, F.S. (Fowzan S), An, Y. (Yu), Anderson, M.-A. (Mary-Anne), Antolik, C. (Caroline), Anyane-Yeboa, K. (Kwame), Atkin, J.F. (Joan), Bartell, T. (Tina), Bernstein, J.A. (Jonathan A.), Beyer, E. (Elizabeth), Blumenthal, I. (Ian), Bongers, E. (Ernie), Brilstra, E.H. (Eva H.), Brown, C.W. (Chester W.), Brüggenwirth, H.T. (Hennie), Callewaert, L., Chiang, C. (Colby), Corning, K. (Ken), Cox, H. (H.), Cuppen, E. (Edwin), Currall, B.B. (Benjamin B.), Cushing, T. (Tom), David, D. (Dezso), Deardorff, M.A. (Matthew), Dheedene, A. (Annelies), D'Hooghe, M. (Marc), Vries, B. (Boukje) de, Earl, D.L. (Dawn L.), Ferguson, H.L. (Heather L.), Fisher, H. (Heather), Fitzpatrick, D.R. (David R.), Gerrol, P. (Pamela), Giachino, D. (Daniela), Glessner, J.T. (Joseph T.), Gliem, T. (Troy), Grady, M. (Margo), Graham, B.H. (Brett H.), Griffis, C. (Cristin), Gripp, K.W. (Karen), Gropman, A.L. (Andrea L.), Hanson-Kahn, A. (Andrea), Harris, D.J. (David J.), Hayden, M.A. (Mark A.), Hill, R. (Rosamund), Hochstenbach, R. (Ron), Hoffman, J.D. (Jodi D.), Hopkin, R., Hubshman, M.W. (Monika W.), Innes, M., Irons, M. (Mira), Irving, M. (Melita), Jacobsen, J.C. (Jessie C.), Janssens, S. (Sandra), Jewett, T. (Tamison), Johnson, J.P. (John P.), Jongmans, M.C.J. (Marjolijn), Kahler, S.G. (Stephen G.), Koolen, D.A. (David), Korzelius, J. (Jerome), Kroisel, P. (Peter), Lacassie, Y. (Yves), Lawless, W. (William), Lemyre, E. (Emmanuelle), Leppig, K. (Kathy), Levin, A.V. (Alex V.), Li, H. (Haibo), Li, H. (Hong), Liao, E.C. (Eric C.), Lim, C. (Cynthia), Lose, E.J. (Edward J.), Lucente, D. (Diane), MacEra, M.J. (Michael J.), Manavalan, P. (Poornima), Mandrile, G. (Giorgia), Marcelis, C.L.M. (Carlo), Margolin, L. (Lauren), Mason, T. (Tamara), Masser-Frye, D. (Diane), McClellan, M.W. (Michael W.), Zepeda Mendoza, C.J. (Cinthya J.), Menten, B., Middelkamp, S. (Sjors), Mikami, L.R. (Liya R.), Moe, E. (Emily), Mohammed, S. (Shabaz), Mononen, T. (Tarja), Mortenson, M.E. (Megan E.), Moya, G. (Graciela), Nieuwint, A.W. (Aggie W.), Ordulu, Z. (Zehra), Parkash, S. (Sandhya), Pauker, S.P. (Susan P.), Pereira, S. (Shahrin), Perrin, D. (Danielle), Phelan, K. (Katy), Piña Aguilar, R.E. (Raul E.), Poddighe, P. (Pino), Pregno, G. (Giulia), Raskin, S. (Salmo), Reis, L. (Linda), Rhead, W. (William), Rita, D. (Debra), Renkens, I. (Ivo), Roelens, F. (Filip), Ruliera, J. (Jayla), Rump, P. (Patrick), Schilit, S.L.P. (Samantha L.P.), Shaheen, R. (Ranad), Sparkes, R. (Rebecca), Spiegel, E. (Erica), Stevens, B. (Blair), Stone, M.R. (Matthew R.), Tagoe, J. (Julia), Thakuria, J.V. (Joseph V.), Bon, B. (Bregje) van, van de Kamp, J.M. (Jiddeke M.), Van Der Burgt, I. (Ineke), Essen, T. (Ton) van, Ravenswaaij-Arts, C.M.A. (Conny) van, Van Roosmalen, M.J. (Markus J.), Vergult, S. (Sarah), Volker-Touw, C.M.L. (Catharina M.L.), Warburton, D. (Dorothy), Waterman, M.J. (Matthew J.), Wiley, S. (Susan), Wilson, A. (Anna), Yerena-De Vega, M.D.L.C.A. (Maria De La Concepcion A), Zori, R.T. (Roberto T.), Levy, B. (Brynn), Brunner, H.G. (Han), Leeuw, N. (Nicole) de, Kloosterman, W.P. (Wigard), Thorland, E.C. (Erik C.), Morton, C.C. (Cynthia), Gusella, J.F. (James), and Talkowski, M.E. (Michael E.)

Abstract

Despite the clinical significance of balanced chromosomal abnormalities (BCAs), their characterization has largely been restricted to cytogenetic resolution. We explored the landscape of BCAs at nucleotide resolution in 273 subjects with a spectrum of congenital anomalies. Whole-genome sequencing revised 93% of karyotypes and demonstrated complexity that was cryptic to karyotyping in 21% of BCAs, highlighting the limitations of conventional cytogenetic approaches. At least 33.9% of BCAs resulted in gene disruption that likely contributed to the developmental phenotype, 5.2% were associated with pathogenic genomic imbalances, and 7.3% disrupted topologically associated domains (TADs) encompassing known syndromic loci. Remarkably, BCA br

Published
2017
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5. Further delineation of the KBG syndrome phenotype caused by ANKRD11 aberrations

Author

Ockeloen, C. (Charlotte), Willemsen, M.H. (Marjolein), Munnik, S.A. (Sonja) de, Bon, B. (Bregje) van, Leeuw, N. (Nicole) de, Verrips, A. (Aad), Kant, S.G. (Sarina), Jones, E.A. (Elizabeth A.), Brunner, H.G., Van Loon, R.L.E. (Rosa), Smeets, E.E.J. (Eric E.J.), Haelst, M.M. (Mieke) van, Haaften, G. (Gijs) van, Nordgren, A. (Ann), Malmgren, H. (Helena), Grigelioniene, G. (Giedre), Vermeer, S.E. (Sarah), Louro, P. (Pedro), Ramos, L. (Lina), Maal, T.J.J. (Thomas J.J.), Heumen, C.C.M. (Céleste) van, Yntema, H.G., Carels, C.E.L. (Carine), Kleefstra, T. (Tjitske), Ockeloen, C. (Charlotte), Willemsen, M.H. (Marjolein), Munnik, S.A. (Sonja) de, Bon, B. (Bregje) van, Leeuw, N. (Nicole) de, Verrips, A. (Aad), Kant, S.G. (Sarina), Jones, E.A. (Elizabeth A.), Brunner, H.G., Van Loon, R.L.E. (Rosa), Smeets, E.E.J. (Eric E.J.), Haelst, M.M. (Mieke) van, Haaften, G. (Gijs) van, Nordgren, A. (Ann), Malmgren, H. (Helena), Grigelioniene, G. (Giedre), Vermeer, S.E. (Sarah), Louro, P. (Pedro), Ramos, L. (Lina), Maal, T.J.J. (Thomas J.J.), Heumen, C.C.M. (Céleste) van, Yntema, H.G., Carels, C.E.L. (Carine), and Kleefstra, T. (Tjitske)

Abstract

Loss-of-function variants in ANKRD11 were identified as the cause of KBG syndrome, an autosomal dominant syndrome with specific dental, neurobehavioural, craniofacial and skeletal

Published
2015
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6. Neuropsychological phenotype of a patient with a de novo 970 kb interstitial deletion in the distal 16p11.2 region

Author

Egger, J.I.M. (Jos), Verhoeven, W.M.A. (Wim), Verbeeck, W. (Wim), Leeuw, N. (Nicole) de, Egger, J.I.M. (Jos), Verhoeven, W.M.A. (Wim), Verbeeck, W. (Wim), and Leeuw, N. (Nicole) de

Abstract

The 16p11.2 microdeletion syndrome is characterized by a wide range of phenotypic expressions and is frequently associated with developmental delay, symptoms from the autism spectrum, epilepsy, congenital anomalies, and obesity. These phenotypes are often related to a proximal 16p11.2 deletion of approximately 600 kb (BP4-BP5) that includes the SH2B1 gene that is reported to be causative for morbid obesity. This more centromeric deletion is most strongly related to autism spectrum susceptibility and is functionally different from the more distal 16p12.2p11.2 region, which includes the so-called atypical 16p11.2 BP2-BP3 deletion (approximately 220 kb) presenting with developmental delay, behavioral problems and mild facial dysmorphisms. Here, an adult male with a long history of maladaptive behaviors is described who was referred for diagnostic assessment of his amotivational features. Extensive neuropsychological examination demonstrated rigid thinking, anxious beliefs, and ideas of reference in the presence of normal intelligence. Microarray analysis demonstrated a de novo 970 kb 16p11.2 BP1-BP4 microdeletion that can be regarded as explanatory for his behavioral profile. It is concluded that microdeletion syndromes are not exclusively related to intellectual disabilities and genetic testing is of putative relevance for the understanding of neuropsychiatric and neuropsychological phenomena.

Published
2014
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7. Copy number variants in a sample of patients with psychotic disorders: Is standard screening relevant for actual clinical practice?

Author

Kerkhof, N.W.A. (Noortje) van de, Feenstra, I. (Ilse), Heijden, F.M.M.A. (Frank) van der, Leeuw, N. (Nicole) de, Pfundt, R. (Rolph), Stöber, G. (Gerald), Egger, J.I.M. (Jos), Verhoeven, W.M.A. (Wim), Kerkhof, N.W.A. (Noortje) van de, Feenstra, I. (Ilse), Heijden, F.M.M.A. (Frank) van der, Leeuw, N. (Nicole) de, Pfundt, R. (Rolph), Stöber, G. (Gerald), Egger, J.I.M. (Jos), and Verhoeven, W.M.A. (Wim)

Abstract

With the introduction of new genetic techniques such as genome-wide array comparative genomic hybridization, studies on the putative genetic etiology of schizophrenia have focused on the detection of copy number variants (CNVs), ie, microdeletions and/or microduplications, that are estimated to be present in up to 3% of patients with schizophrenia. In this study, out of a sample of 100 patients with psychotic disorders, 80 were investigated by array for the presence of CNVs. The assessment of the severity of psychiatric symptoms was performed using standardized instruments and ICD-10 was applied for diagnostic classification. In three patients, a submicroscopic CNV was demonstrated, one with a loss in 1q21.1 and two with a gain in 1p13.3 and 7q11.2, respectively. The association between these or other CNVs and schizophrenia or schizophrenia-like psychoses and their clinical implications still remain equivocal. While the CNV affected genes may enhance the vulnerability for psychiatric disorders via effects on neuronal architecture, these insights have not resulted in major changes in clinical practice as yet. Therefore, genome-wide array analysis should presently be restricted to those patients in whom psychotic symptoms are paired with other signs, particularly dysmorphisms and intellectual impairment.

Published
2012
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