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5 results on '"Sluijs, P.J. van der"'

1. PhenoScore quantifies phenotypic variation for rare genetic diseases by combining facial analysis with other clinical features using a machine-learning framework

Author

Dingemans, A.J.M., Hinne, M., Truijen, K.M.G., Goltstein, C.M.J., Reeuwijk, J. van, Leeuw, N. de, Schuurs-Hoeijmakers, J.H.M., Pfundt, R.P., Diets, I.J., Hoed, J. den, Boer, E. de, Spek, J. van der, Bon, B.W.M. van, Ockeloen, C.W., Vulto-van Silfhout, A.T., Kleefstra, T., Koolen, D.A., Campeau, P.M., Palmer, E.E., Esch, H. van, Lyon, G.J., Alkuraya, F.S., Rauch, A., Marom, R., Baralle, D., Sluijs, P.J. van der, Santen, G.W.E., Kooy, R.F., Gerven, M.A.J. van, Vissers, L.E.L.M., Vries, L.B.A. de, Dingemans, A.J.M., Hinne, M., Truijen, K.M.G., Goltstein, C.M.J., Reeuwijk, J. van, Leeuw, N. de, Schuurs-Hoeijmakers, J.H.M., Pfundt, R.P., Diets, I.J., Hoed, J. den, Boer, E. de, Spek, J. van der, Bon, B.W.M. van, Ockeloen, C.W., Vulto-van Silfhout, A.T., Kleefstra, T., Koolen, D.A., Campeau, P.M., Palmer, E.E., Esch, H. van, Lyon, G.J., Alkuraya, F.S., Rauch, A., Marom, R., Baralle, D., Sluijs, P.J. van der, Santen, G.W.E., Kooy, R.F., Gerven, M.A.J. van, Vissers, L.E.L.M., and Vries, L.B.A. de

Abstract

07 augustus 2023, Item does not contain fulltext, Several molecular and phenotypic algorithms exist that establish genotype–phenotype correlations, including facial recognition tools. However, no unified framework that investigates both facial data and other phenotypic data directly from individuals exists. We developed PhenoScore: an open-source, artificial intelligence-based phenomics framework, combining facial recognition technology with Human Phenotype Ontology data analysis to quantify phenotypic similarity. Here we show PhenoScore’s ability to recognize distinct phenotypic entities by establishing recognizable phenotypes for 37 of 40 investigated syndromes against clinical features observed in individuals with other neurodevelopmental disorders and show it is an improvement on existing approaches. PhenoScore provides predictions for individuals with variants of unknown significance and enables sophisticated genotype–phenotype studies by testing hypotheses on possible phenotypic (sub)groups. PhenoScore confirmed previously known phenotypic subgroups caused by variants in the same gene for SATB1, SETBP1 and DEAF1 and provides objective clinical evidence for two distinct ADNP-related phenotypes, already established functionally.

Published
2023

2. Elucidating the clinical and molecular spectrum of SMARCC2-associated NDD in a cohort of 65 affected individuals.

Author

Bosch, E., Popp, B., Güse, E., Skinner, C., Sluijs, P.J. van der, Maystadt, I., Pinto, Ameet J., Renieri, A., Bruno, L.P., Granata, S., Marcelis, C.L., Baysal, Ö., Hartwich, D., Holthöfer, L., Isidor, B., Cogne, B., Wieczorek, D., Capra, V., Scala, M., Marco, P. De, Ognibene, M., Jamra, R.A., Platzer, K., Carter, L.B., Kuismin, O., Haeringen, A. van, Maroofian, R., Valenzuela, I., Cuscó, I., Martinez-Agosto, J.A., Rabani, A.M., Mefford, H.C., Pereira, E.M., Close, C., Anyane-Yeboa, K., Wagner, M., Hannibal, M.C., Zacher, P., Thiffault, I., Beunders, G., Umair, M., Bhola, P.T., McGinnis, E., Millichap, J., Kamp, J.M. van de, Prijoles, E.J., Dobson, A., Shillington, A., Graham, B.H., Garcia, E.J., Galindo, M.K., Ropers, F.G., Nibbeling, E.A., Hubbard, G., Karimov, C., Goj, G., Bend, R., Rath, J., Morrow, M.M., Millan, F., Salpietro, V., Torella, A., Nigro, V., Kurki, M., Stevenson, R.E., Santen, G.W.E., Zweier, M., Campeau, P.M., Severino, M., Reis, A., Accogli, A., Vasileiou, G., Bosch, E., Popp, B., Güse, E., Skinner, C., Sluijs, P.J. van der, Maystadt, I., Pinto, Ameet J., Renieri, A., Bruno, L.P., Granata, S., Marcelis, C.L., Baysal, Ö., Hartwich, D., Holthöfer, L., Isidor, B., Cogne, B., Wieczorek, D., Capra, V., Scala, M., Marco, P. De, Ognibene, M., Jamra, R.A., Platzer, K., Carter, L.B., Kuismin, O., Haeringen, A. van, Maroofian, R., Valenzuela, I., Cuscó, I., Martinez-Agosto, J.A., Rabani, A.M., Mefford, H.C., Pereira, E.M., Close, C., Anyane-Yeboa, K., Wagner, M., Hannibal, M.C., Zacher, P., Thiffault, I., Beunders, G., Umair, M., Bhola, P.T., McGinnis, E., Millichap, J., Kamp, J.M. van de, Prijoles, E.J., Dobson, A., Shillington, A., Graham, B.H., Garcia, E.J., Galindo, M.K., Ropers, F.G., Nibbeling, E.A., Hubbard, G., Karimov, C., Goj, G., Bend, R., Rath, J., Morrow, M.M., Millan, F., Salpietro, V., Torella, A., Nigro, V., Kurki, M., Stevenson, R.E., Santen, G.W.E., Zweier, M., Campeau, P.M., Severino, M., Reis, A., Accogli, A., and Vasileiou, G.

Abstract

Contains fulltext : 299984.pdf (Publisher’s version ) (Open Access), PURPOSE: Coffin-Siris and Nicolaides-Baraitser syndromes are recognizable neurodevelopmental disorders caused by germline variants in BAF complex subunits. The SMARCC2 BAFopathy was recently reported. Herein, we present clinical and molecular data on a large cohort. METHODS: Clinical symptoms for 41 novel and 24 previously published affected individuals were analyzed using the Human Phenotype Ontology. For genotype-phenotype correlations, molecular data were standardized and grouped into non-truncating and likely gene-disrupting (LGD) variants. Missense variant protein expression and BAF-subunit interactions were examined using 3D protein modeling, co-immunoprecipitation, and proximity-ligation assays. RESULTS: Neurodevelopmental delay with intellectual disability, muscular hypotonia, and behavioral disorders were the major manifestations. Clinical hallmarks of BAFopathies were rare. Clinical presentation differed significantly, with LGD variants being predominantly inherited and associated with mildly reduced or normal cognitive development, whereas non-truncating variants were mostly de novo and presented with severe developmental delay. These distinct manifestations and non-truncating variant clustering in functional domains suggest different pathomechanisms. In vitro testing showed decreased protein expression for N-terminal missense variants similar to LGD. CONCLUSION: This study improved SMARCC2 variant classification and identified discernible SMARCC2-associated phenotypes for LGD and non-truncating variants, which were distinct from other BAFopathies. The pathomechanism of most non-truncating variants has yet to be investigated., 01 november 2023

Published
2023

3. Discovering a new part of the phenotypic spectrum of Coffin-Siris syndrome in a fetal cohort

Author

Sluijs, P.J. van der, Joosten, Marieke, Alby, C., Attié-Bitach, T., Gilmore, K., Dubourg, C., Fradin, M., Wang, T., Kurtz-Nelson, E.C., Ahlers, K.P., Arts, P., Barnett, C.P., Ashfaq, M., Baban, A., Born, M. van den, Borrie, S., Busa, T., Byrne, A., Carriero, M., Cesario, C., Chong, K., Cueto-González, A.M., Dempsey, J.C., Diderich, K.E.M., Doherty, D., Farholt, S., Gerkes, E.H., Gorokhova, S., Govaerts, L.C.P., Gregersen, P.A., Hickey, S.E., Lefebvre, M., Mari, F., Martinovic, Jelena, Northrup, H., O'Leary, M., Parbhoo, K., Patrier, S., Popp, B., Santos-Simarro, F., Stoltenburg, C., Thauvin-Robinet, C., Thompson, E., Vulto-van Silfhout, A.T., Zahir, F.R., Scott, H.S., Earl, R.K., Eichler, E.E., Vora, N.L., Wilnai, Y., Giordano, J.L., Wapner, R.J., Rosenfeld, J.A., Haak, M.C., Santen, G.W.E., Sluijs, P.J. van der, Joosten, Marieke, Alby, C., Attié-Bitach, T., Gilmore, K., Dubourg, C., Fradin, M., Wang, T., Kurtz-Nelson, E.C., Ahlers, K.P., Arts, P., Barnett, C.P., Ashfaq, M., Baban, A., Born, M. van den, Borrie, S., Busa, T., Byrne, A., Carriero, M., Cesario, C., Chong, K., Cueto-González, A.M., Dempsey, J.C., Diderich, K.E.M., Doherty, D., Farholt, S., Gerkes, E.H., Gorokhova, S., Govaerts, L.C.P., Gregersen, P.A., Hickey, S.E., Lefebvre, M., Mari, F., Martinovic, Jelena, Northrup, H., O'Leary, M., Parbhoo, K., Patrier, S., Popp, B., Santos-Simarro, F., Stoltenburg, C., Thauvin-Robinet, C., Thompson, E., Vulto-van Silfhout, A.T., Zahir, F.R., Scott, H.S., Earl, R.K., Eichler, E.E., Vora, N.L., Wilnai, Y., Giordano, J.L., Wapner, R.J., Rosenfeld, J.A., Haak, M.C., and Santen, G.W.E.

Abstract

Item does not contain fulltext, PURPOSE: Genome-wide sequencing is increasingly being performed during pregnancy to identify the genetic cause of congenital anomalies. The interpretation of prenatally identified variants can be challenging and is hampered by our often limited knowledge of prenatal phenotypes. To better delineate the prenatal phenotype of Coffin-Siris syndrome (CSS), we collected clinical data from patients with a prenatal phenotype and a pathogenic variant in one of the CSS-associated genes. METHODS: Clinical data was collected through an extensive web-based survey. RESULTS: We included 44 patients with a variant in a CSS-associated gene and a prenatal phenotype; 9 of these patients have been reported before. Prenatal anomalies that were frequently observed in our cohort include hydrocephalus, agenesis of the corpus callosum, hypoplastic left heart syndrome, persistent left vena cava, diaphragmatic hernia, renal agenesis, and intrauterine growth restriction. Anal anomalies were frequently identified after birth in patients with ARID1A variants (6/14, 43%). Interestingly, pathogenic ARID1A variants were much more frequently identified in the current prenatal cohort (16/44, 36%) than in postnatal CSS cohorts (5%-9%). CONCLUSION: Our data shed new light on the prenatal phenotype of patients with pathogenic variants in CSS genes.

Published
2022

4. Discovering a new part of the phenotypic spectrum of Coffin-Siris syndrome in a fetal cohort

Author

Sluijs, P.J. van der, Joosten, Marieke, Alby, C., Attié-Bitach, T., Gilmore, K., Dubourg, C., Fradin, M., Wang, T., Kurtz-Nelson, E.C., Ahlers, K.P., Arts, P., Barnett, C.P., Ashfaq, M., Baban, A., Born, M. van den, Borrie, S., Busa, T., Byrne, A., Carriero, M., Cesario, C., Chong, K., Cueto-González, A.M., Dempsey, J.C., Diderich, K.E.M., Doherty, D., Farholt, S., Gerkes, E.H., Gorokhova, S., Govaerts, L.C.P., Gregersen, P.A., Hickey, S.E., Lefebvre, M., Mari, F., Martinovic, Jelena, Northrup, H., O'Leary, M., Parbhoo, K., Patrier, S., Popp, B., Santos-Simarro, F., Stoltenburg, C., Thauvin-Robinet, C., Thompson, E., Vulto-van Silfhout, A.T., Zahir, F.R., Scott, H.S., Earl, R.K., Eichler, E.E., Vora, N.L., Wilnai, Y., Giordano, J.L., Wapner, R.J., Rosenfeld, J.A., Haak, M.C., Santen, G.W.E., Sluijs, P.J. van der, Joosten, Marieke, Alby, C., Attié-Bitach, T., Gilmore, K., Dubourg, C., Fradin, M., Wang, T., Kurtz-Nelson, E.C., Ahlers, K.P., Arts, P., Barnett, C.P., Ashfaq, M., Baban, A., Born, M. van den, Borrie, S., Busa, T., Byrne, A., Carriero, M., Cesario, C., Chong, K., Cueto-González, A.M., Dempsey, J.C., Diderich, K.E.M., Doherty, D., Farholt, S., Gerkes, E.H., Gorokhova, S., Govaerts, L.C.P., Gregersen, P.A., Hickey, S.E., Lefebvre, M., Mari, F., Martinovic, Jelena, Northrup, H., O'Leary, M., Parbhoo, K., Patrier, S., Popp, B., Santos-Simarro, F., Stoltenburg, C., Thauvin-Robinet, C., Thompson, E., Vulto-van Silfhout, A.T., Zahir, F.R., Scott, H.S., Earl, R.K., Eichler, E.E., Vora, N.L., Wilnai, Y., Giordano, J.L., Wapner, R.J., Rosenfeld, J.A., Haak, M.C., and Santen, G.W.E.

Abstract

Contains fulltext : 282685.pdf (Publisher’s version ) (Open Access), PURPOSE: Genome-wide sequencing is increasingly being performed during pregnancy to identify the genetic cause of congenital anomalies. The interpretation of prenatally identified variants can be challenging and is hampered by our often limited knowledge of prenatal phenotypes. To better delineate the prenatal phenotype of Coffin-Siris syndrome (CSS), we collected clinical data from patients with a prenatal phenotype and a pathogenic variant in one of the CSS-associated genes. METHODS: Clinical data was collected through an extensive web-based survey. RESULTS: We included 44 patients with a variant in a CSS-associated gene and a prenatal phenotype; 9 of these patients have been reported before. Prenatal anomalies that were frequently observed in our cohort include hydrocephalus, agenesis of the corpus callosum, hypoplastic left heart syndrome, persistent left vena cava, diaphragmatic hernia, renal agenesis, and intrauterine growth restriction. Anal anomalies were frequently identified after birth in patients with ARID1A variants (6/14, 43%). Interestingly, pathogenic ARID1A variants were much more frequently identified in the current prenatal cohort (16/44, 36%) than in postnatal CSS cohorts (5%-9%). CONCLUSION: Our data shed new light on the prenatal phenotype of patients with pathogenic variants in CSS genes.

Published
2022

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