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23 results on '"Dingemans, A.J.M."'

1. ARID1B-related disorder in 87 adults: Natural history and self-sustainability

Author

van der Sluijs, P.J., Gösgens, M., Dingemans, A.J.M., Striano, P., Riva, A., Mignot, C., Faudet, A., Vasileiou, G., Walther, M., Schrier Vergano, S.A., Alders, M., Alkuraya, F.S., Alorainy, I., Alsaif, H.S., Anderlid, B., Bache, I., van Beek, I., Blanluet, M., van Bon, B.W., Brunet, T., Brunner, H., Carriero, M.L., Charles, P., Chatron, N., Coccia, E., Dubourg, C., Earl, R.K., Eichler, E.E., Faivre, L., Foulds, N., Graziano, C., Guerrot, A.M., Hashem, M.O., Heide, S., Heron, D., Hickey, S.E., Hopman, S.M.J., Kattentidt-Mouravieva, A., Kerkhof, J., Klein Wassink-Ruiter, J.S., Kurtz-Nelson, E.C., Kušíková, K., Kvarnung, M., Lecoquierre, F., Leszinski, G.S., Loberti, L., Magoulas, P.L., Mari, F., Maystadt, I., Merla, G., Milunsky, J.M., Moortgat, S., Nicolas, G., Leary, M.O.’, Odent, S., Ozmore, J.R., Parbhoo, K., Pfundt, R., Piccione, M., Pinto, A.M., Popp, B., Putoux, A., Rehm, H.L., Reis, A., Renieri, A., Rosenfeld, J.A., Rossi, M., Salzano, E., Saugier-Veber, P., Seri, M., Severi, G., Sonmez, F.M., Strobl-Wildemann, G., Stuurman, K.E., Uctepe, E., Van Esch, H., Vitetta, G., de Vries, B.B.A., Wahl, D., Wang, T., Zacher, P., Heitink, K.R., Ropers, F.G., Steenbeek, D., Rybak, T., and Santen, G.W.E.

Published
2024
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2. Next-generation phenotyping in neurodevelopmental disorders: Applications of artificial intelligence in clinical genetics

Author

Vries, L.B.A. de, Gerven, M.A.J. van, Vissers, L.E.L.M., Hinne, M., Dingemans, A.J.M., Vries, L.B.A. de, Gerven, M.A.J. van, Vissers, L.E.L.M., Hinne, M., and Dingemans, A.J.M.

Abstract

Contains fulltext : 306760.pdf (Publisher’s version ) (Open Access), Radboud University, 12 juni 2024, Promotores : Vries, L.B.A. de, Gerven, M.A.J. van, Vissers, L.E.L.M. Co-promotor : Hinne, M., 236 p.

Published
2024

4. DNA methylation episignature for Witteveen-Kolk syndrome due to SIN3A haploinsufficiency

Author

Coenen-van der Spek, J., Relator, Raissa, Kerkhof, J., McConkey, H., Levy, M.A., Tedder, M., Kolk, Sharon M., Dingemans, A.J.M., Pfundt, R.P., Kleefstra, T., Butler, K., Coenen-van der Spek, J., Relator, Raissa, Kerkhof, J., McConkey, H., Levy, M.A., Tedder, M., Kolk, Sharon M., Dingemans, A.J.M., Pfundt, R.P., Kleefstra, T., and Butler, K.

Abstract

Contains fulltext : 290129.pdf (Publisher’s version ) (Closed access)

Published
2023

6. 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

7. Phenotype based prediction of exome sequencing outcome using machine learning for neurodevelopmental disorders

Author

Dingemans, A.J.M., Hinne, M., Jansen, S, Reeuwijk, J. van, Leeuw, N. de, Pfundt, R.P., Bon, B.W.M. van, Vulto-van Silfhout, A.T., Kleefstra, T., Koolen, D.A., Gerven, M.A.J. van, Vissers, L.E.L.M., Vries, L.B.A. de, Dingemans, A.J.M., Hinne, M., Jansen, S, Reeuwijk, J. van, Leeuw, N. de, Pfundt, R.P., Bon, B.W.M. van, Vulto-van Silfhout, A.T., Kleefstra, T., Koolen, D.A., Gerven, M.A.J. van, Vissers, L.E.L.M., and Vries, L.B.A. de

Abstract

Item does not contain fulltext, Purpose: Although the introduction of exome sequencing (ES) has led to the diagnosis of a significant portion of patients with neurodevelopmental disorders (NDDs), the diagnostic yield in actual clinical practice has remained stable at approximately 30%. We hypothesized that improving the selection of patients to test on the basis of their phenotypic presentation will increase diagnostic yield and therefore reduce unnecessary genetic testing. Methods: We tested 4 machine learning methods and developed PredWES from these: a statistical model predicting the probability of a positive ES result solely on the basis of the phenotype of the patient. Results: We first trained the tool on 1663 patients with NDDs and subsequently showed that diagnostic ES on the top 10% of patients with the highest probability of a positive ES result would provide a diagnostic yield of 56%, leading to a notable 114% increase. Inspection of our model revealed that for patients with NDDs, comorbid abnormal (lower) muscle tone and microcephaly positively correlated with a conclusive ES diagnosis, whereas autism was negatively associated with a molecular diagnosis. Conclusion: In conclusion, PredWES allows prioritizing patients with NDDs eligible for diagnostic ES on the basis of their phenotypic presentation to increase the diagnostic yield, making a more efficient use of health care resources.

Published
2022

8. Phenotype based prediction of WES outcome using machine learning

Author

Dingemans, A.J.M., Hinne, M., Jansen, S, Reeuwijk, J. van, Leeuw, N. de, Pfundt, R.P., Bon, B.W.M. van, Vulto-van Silfhout, A.T., Kleefstra, T., Koolen, D.A., Gerven, M.A.J. van, Vissers, L.E.L.M., Vries, L.B.A. de, Dingemans, A.J.M., Hinne, M., Jansen, S, Reeuwijk, J. van, Leeuw, N. de, Pfundt, R.P., Bon, B.W.M. van, Vulto-van Silfhout, A.T., Kleefstra, T., Koolen, D.A., Gerven, M.A.J. van, Vissers, L.E.L.M., and Vries, L.B.A. de

Abstract

Contains fulltext : 249711.pdf (Publisher’s version ) (Closed access)

Published
2022

9. Establishing the phenotypic spectrum of ZTTK syndrome by analysis of 52 individuals with variants in SON

Author

Dingemans, A.J.M., Truijen, K.M.G., Kim, J.H., Alaçam, Z., Faivre, L., Collins, K.M., Gerkes, E.H., Haelst, M. van, Laar, I. van de, Lindstrom, K., Nizon, M., Pauling, J., Heropolitańska-Pliszka, E., Plomp, A.S., Racine, C., Sachdev, R., Sinnema, M., Skranes, J., Veenstra-Knol, Hermine E., Verberne, E.A., Vulto-van Silfhout, A.T., Wilsterman, M.E., Ahn, E.E., Vries, B.B.A. de, Vissers, L.E.L.M., Dingemans, A.J.M., Truijen, K.M.G., Kim, J.H., Alaçam, Z., Faivre, L., Collins, K.M., Gerkes, E.H., Haelst, M. van, Laar, I. van de, Lindstrom, K., Nizon, M., Pauling, J., Heropolitańska-Pliszka, E., Plomp, A.S., Racine, C., Sachdev, R., Sinnema, M., Skranes, J., Veenstra-Knol, Hermine E., Verberne, E.A., Vulto-van Silfhout, A.T., Wilsterman, M.E., Ahn, E.E., Vries, B.B.A. de, and Vissers, L.E.L.M.

Abstract

Contains fulltext : 248367.pdf (Publisher’s version ) (Closed access), Zhu-Tokita-Takenouchi-Kim (ZTTK) syndrome, an intellectual disability syndrome first described in 2016, is caused by heterozygous loss-of-function variants in SON. Its encoded protein promotes pre-mRNA splicing of many genes essential for development. Whereas individual phenotypic traits have previously been linked to erroneous splicing of SON target genes, the phenotypic spectrum and the pathogenicity of missense variants have not been further evaluated. We present the phenotypic abnormalities in 52 individuals, including 17 individuals who have not been reported before. In total, loss-of-function variants were detected in 49 individuals (de novo in 47, inheritance unknown in 2), and in 3, a missense variant was observed (2 de novo, 1 inheritance unknown). Phenotypic abnormalities, systematically collected and analyzed in Human Phenotype Ontology, were found in all organ systems. Significant inter-individual phenotypic variability was observed, even in individuals with the same recurrent variant (n = 13). SON haploinsufficiency was previously shown to lead to downregulation of downstream genes, contributing to specific phenotypic features. Similar functional analysis for one missense variant, however, suggests a different mechanism than for heterozygous loss-of-function. Although small in numbers and while pathogenicity of these variants is not certain, these data allow for speculation whether de novo missense variants cause ZTTK syndrome via another mechanism, or a separate overlapping syndrome. In conclusion, heterozygous loss-of-function variants in SON define a recognizable syndrome, ZTTK, associated with a broad, severe phenotypic spectrum, characterized by a large inter-individual variability. These observations provide essential information for affected individuals, parents, and healthcare professionals to ensure appropriate clinical management.

Published
2022

10. The phenotypic spectrum and genotype-phenotype correlations in 106 patients with variants in major autism gene CHD8

Author

Dingemans, A.J.M., Truijen, Kim M.G., Ven, Sam van de, Bernier, R., Bongers, E.M.H.F., Bouman, Arjan, Kleefstra, T., Vissers, L.E.L.M., Vries, B.B.A. de, Dingemans, A.J.M., Truijen, Kim M.G., Ven, Sam van de, Bernier, R., Bongers, E.M.H.F., Bouman, Arjan, Kleefstra, T., Vissers, L.E.L.M., and Vries, B.B.A. de

Abstract

Contains fulltext : 282761.pdf (Publisher’s version ) (Open Access)

Published
2022

11. Missense variants in ANKRD11 cause KBG syndrome by impairment of stability or transcriptional activity of the encoded protein

Author

Boer, E. de, Ockeloen, C.W., Kampen, R.A., Hampstead, J.E., Dingemans, A.J.M., Rots, D., Pfundt, R.P., Reeuwijk, J. van, Gilissen, C.F.H.A., Vissers, L.E.L.M., Wong, M., Fisher, S.E., Kleefstra, T., Boer, E. de, Ockeloen, C.W., Kampen, R.A., Hampstead, J.E., Dingemans, A.J.M., Rots, D., Pfundt, R.P., Reeuwijk, J. van, Gilissen, C.F.H.A., Vissers, L.E.L.M., Wong, M., Fisher, S.E., and Kleefstra, T.

Abstract

Contains fulltext : 284428.pdf (Publisher’s version ) (Open Access)

Published
2022

12. KAT6A Syndrome

Author

Kennedy, J., Goudie, D., Blair, E., Chandler, K., Joss, S., McKay, V., Green, A., Armstrong, R., Lees, M., Kamien, B., Hopper, B., Tan, T.Y., Yap, P., Stark, Z., Okamoto, N., Miyake, N., Matsumoto, N., Macnamara, E., Murphy, J.L., McCormick, E., Hakonarson, H., Falk, M.J., Li, D., Blackburn, P., Klee, E., Babovic-Vuksanovic, D., Schelley, S., Hudgins, L., Kant, S., Isidor, B., Cogne, B., Bradbury, K., Williams, M., Patel, C., Heussler, H., Duff-Farrier, C., Lakeman, P., Scurr, I., Kini, U., Elting, M., Reijnders, M., Schuurs-Hoeijmakers, J., Wafik, M., Blomhoff, A., Ruivenkamp, C.A.L., Nibbeling, E., Dingemans, A.J.M., Douine, E.D., Nelson, S.F., Hempel, M., Bierhals, T., Lessel, D., Johannsen, J., Arboleda, V.A., Newbury-Ecob, R., and DDD Study

Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020
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13. Comprehensive study of 28 individuals with SIN3A-related disorder underscoring the associated mild cognitive and distinctive facial phenotype

Author

Balasubramanian, M., Dingemans, A.J.M., Albaba, S., Richardson, R., Yates, T.M., Cox, H., Douzgou, S., Armstrong, R., Sansbury, F.H., Burke, K.B., Fry, A.E., Ragge, N., Sharif, S., Foster, A., Sandre-Giovannoli, A. De, Elouej, S., Vasudevan, P., Mansour, S., Wilson, K., Stewart, H., Heide, S. van der, Nava, C., Keren, B., Demirdas, S., Brooks, A.S., Vincent, M., Isidor, B., Küry, S., Schouten, M.I., Leenders, E.K.S.M., Chung, W.K., Haeringen, A.V., Scheffner, T., Debray, F.G., White, S.M., Palafoll, M.I.V., Pfundt, R.P., Newbury-Ecob, R., Kleefstra, T., Balasubramanian, M., Dingemans, A.J.M., Albaba, S., Richardson, R., Yates, T.M., Cox, H., Douzgou, S., Armstrong, R., Sansbury, F.H., Burke, K.B., Fry, A.E., Ragge, N., Sharif, S., Foster, A., Sandre-Giovannoli, A. De, Elouej, S., Vasudevan, P., Mansour, S., Wilson, K., Stewart, H., Heide, S. van der, Nava, C., Keren, B., Demirdas, S., Brooks, A.S., Vincent, M., Isidor, B., Küry, S., Schouten, M.I., Leenders, E.K.S.M., Chung, W.K., Haeringen, A.V., Scheffner, T., Debray, F.G., White, S.M., Palafoll, M.I.V., Pfundt, R.P., Newbury-Ecob, R., and Kleefstra, T.

Abstract

Contains fulltext : 245024.pdf (Publisher’s version ) (Open Access), Witteveen-Kolk syndrome (OMIM 613406) is a recently defined neurodevelopmental syndrome caused by heterozygous loss-of-function variants in SIN3A. We define the clinical and neurodevelopmental phenotypes related to SIN3A-haploinsufficiency in 28 unreported patients. Patients with SIN3A variants adversely affecting protein function have mild intellectual disability, growth and feeding difficulties. Involvement of a multidisciplinary team including a geneticist, paediatrician and neurologist should be considered in managing these patients. Patients described here were identified through a combination of clinical evaluation and gene matching strategies (GeneMatcher and Decipher). All patients consented to participate in this study. Mean age of this cohort was 8.2 years (17 males, 11 females). Out of 16 patients ≥ 8 years old assessed, eight (50%) had mild intellectual disability (ID), four had moderate ID (22%), and one had severe ID (6%). Four (25%) did not have any cognitive impairment. Other neurological symptoms such as seizures (4/28) and hypotonia (12/28) were common. Behaviour problems were reported in a minority. In patients ≥2 years, three were diagnosed with Autism Spectrum Disorder (ASD) and four with Attention Deficit Hyperactivity Disorder (ADHD). We report 27 novel variants and one previously reported variant. 24 were truncating variants; three were missense variants and one large in-frame gain including exons 10-12.

Published
2021

14. A Case Series of Familial ARID1B Variants Illustrating Variable Expression and Suggestions to Update the ACMG Criteria

Author

Sluijs, Pleuntje J. van der, Alders, M., Dingemans, A.J.M., Parbhoo, Kareesma, Bon, B.W. van, Dempsey, J.C., Vries, B.B.A. de, Maystadt, I., Santen, G.W.E., Sluijs, Pleuntje J. van der, Alders, M., Dingemans, A.J.M., Parbhoo, Kareesma, Bon, B.W. van, Dempsey, J.C., Vries, B.B.A. de, Maystadt, I., and Santen, G.W.E.

Abstract

Contains fulltext : 237017.pdf (Publisher’s version ) (Open Access)

Published
2021

15. Mutation-specific pathophysiological mechanisms define different neurodevelopmental disorders associated with SATB1 dysfunction

Author

Hoed, J. den, Boer, E. de, Voisin, N., Dingemans, A.J.M., Guex, N., Wiel, L.J.M. van de, Nellaker, C., Amudhavalli, S.M., Banka, S., Bena, F.S., Ben-Zeev, B., Bonagura, V.R., Bruel, A.L., Brunet, T., Brunner, H.G., Chew, H.B., Chrast, J., Cimbalistienė, L., Coon, H., Délot, E.C., Démurger, F., Denommé-Pichon, A.S., Depienne, C., Donnai, D., Dyment, D.A., Elpeleg, O., Faivre, L., Gilissen, C.F., Granger, L., Haber, B., Hachiya, Y., Abedi, Y.H., Hanebeck, J., Hehir-Kwa, J.Y., Horist, B., Itai, T., Jackson, A., Jewell, R., Jones, K.L., Joss, S., Kashii, H., Kato, M., Kattentidt-Mouravieva, A.A., Kok, F., Kotzaeridou, U., Krishnamurthy, V., Kučinskas, V., Kuechler, A., Lavillaureix, A., Liu, P, Manwaring, L., Matsumoto, N., Mazel, B., McWalter, K., Meiner, V., Mikati, M.A., Miyatake, S., Mizuguchi, T., Moey, L.H., Mohammed, S, Mor-Shaked, H., Mountford, H., Newbury-Ecob, R., Odent, S., Orec, L., Osmond, M., Palculict, T.B., Parker, M., Petersen, A.K., Pfundt, R.P., Preikšaitienė, E., Radtke, K., Ranza, E., Rosenfeld, J.A., Santiago-Sim, T., Schwager, C., Sinnema, M., Snijders Blok, L., Spillmann, R.C., Stegmann, A.P.A., Thiffault, I., Tran, L., Vaknin-Dembinsky, A., Vedovato-Dos-Santos, J.H., Schrier Vergano, S.A., Vilain, E., Vitobello, A., Wagner, M., Waheeb, A., Willing, M., Zuccarelli, B., Kini, U., Newbury, D.F., Kleefstra, T., Reymond, A., Fisher, S.E., Vissers, L.E.L.M., Hoed, J. den, Boer, E. de, Voisin, N., Dingemans, A.J.M., Guex, N., Wiel, L.J.M. van de, Nellaker, C., Amudhavalli, S.M., Banka, S., Bena, F.S., Ben-Zeev, B., Bonagura, V.R., Bruel, A.L., Brunet, T., Brunner, H.G., Chew, H.B., Chrast, J., Cimbalistienė, L., Coon, H., Délot, E.C., Démurger, F., Denommé-Pichon, A.S., Depienne, C., Donnai, D., Dyment, D.A., Elpeleg, O., Faivre, L., Gilissen, C.F., Granger, L., Haber, B., Hachiya, Y., Abedi, Y.H., Hanebeck, J., Hehir-Kwa, J.Y., Horist, B., Itai, T., Jackson, A., Jewell, R., Jones, K.L., Joss, S., Kashii, H., Kato, M., Kattentidt-Mouravieva, A.A., Kok, F., Kotzaeridou, U., Krishnamurthy, V., Kučinskas, V., Kuechler, A., Lavillaureix, A., Liu, P, Manwaring, L., Matsumoto, N., Mazel, B., McWalter, K., Meiner, V., Mikati, M.A., Miyatake, S., Mizuguchi, T., Moey, L.H., Mohammed, S, Mor-Shaked, H., Mountford, H., Newbury-Ecob, R., Odent, S., Orec, L., Osmond, M., Palculict, T.B., Parker, M., Petersen, A.K., Pfundt, R.P., Preikšaitienė, E., Radtke, K., Ranza, E., Rosenfeld, J.A., Santiago-Sim, T., Schwager, C., Sinnema, M., Snijders Blok, L., Spillmann, R.C., Stegmann, A.P.A., Thiffault, I., Tran, L., Vaknin-Dembinsky, A., Vedovato-Dos-Santos, J.H., Schrier Vergano, S.A., Vilain, E., Vitobello, A., Wagner, M., Waheeb, A., Willing, M., Zuccarelli, B., Kini, U., Newbury, D.F., Kleefstra, T., Reymond, A., Fisher, S.E., and Vissers, L.E.L.M.

Abstract

Contains fulltext : 231687.pdf (Publisher’s version ) (Closed access), Whereas large-scale statistical analyses can robustly identify disease-gene relationships, they do not accurately capture genotype-phenotype correlations or disease mechanisms. We use multiple lines of independent evidence to show that different variant types in a single gene, SATB1, cause clinically overlapping but distinct neurodevelopmental disorders. Clinical evaluation of 42 individuals carrying SATB1 variants identified overt genotype-phenotype relationships, associated with different pathophysiological mechanisms, established by functional assays. Missense variants in the CUT1 and CUT2 DNA-binding domains result in stronger chromatin binding, increased transcriptional repression, and a severe phenotype. In contrast, variants predicted to result in haploinsufficiency are associated with a milder clinical presentation. A similarly mild phenotype is observed for individuals with premature protein truncating variants that escape nonsense-mediated decay, which are transcriptionally active but mislocalized in the cell. Our results suggest that in-depth mutation-specific genotype-phenotype studies are essential to capture full disease complexity and to explain phenotypic variability.

Published
2021

16. Quantitative facial phenotyping for Koolen-de Vries and 22q11.2 deletion syndrome

Author

Dingemans, A.J.M., Stremmelaar, D.E., Donk, R. van der, Vissers, L.E.L.M., Koolen, D.A., Rump, P., Hehir-Kwa, J.Y., Vries, B.B.A. de, Dingemans, A.J.M., Stremmelaar, D.E., Donk, R. van der, Vissers, L.E.L.M., Koolen, D.A., Rump, P., Hehir-Kwa, J.Y., and Vries, B.B.A. de

Abstract

Contains fulltext : 237899.pdf (Publisher’s version ) (Closed access), The Koolen-de Vries syndrome (KdVS) is a multisystem syndrome with variable facial features caused by a 17q21.31 microdeletion or KANSL1 truncating variant. As the facial gestalt of KdVS has resemblance with the gestalt of the 22q11.2 deletion syndrome (22q11.2DS), we assessed whether our previously described hybrid quantitative facial phenotyping algorithm could distinguish between these two syndromes, and whether there is a facial difference between the molecular KdVS subtypes. We applied our algorithm to 2D photographs of 97 patients with KdVS (78 microdeletions, 19 truncating variants (likely) causing KdVS) and 48 patients with 22q11.2DS as well as age, gender and ethnicity matched controls with intellectual disability (n = 145). The facial gestalts of KdVS and 22q11.2DS were both recognisable through significant clustering by the hybrid model, yet different from one another (p = 7.5 × 10(-10) and p = 0.0052, respectively). Furthermore, the facial gestalts of KdVS caused by a 17q21.31 microdeletion and KANSL1 truncating variant (likely) causing KdVS were indistinguishable (p = 0.981 and p = 0.130). Further application to three patients with a variant of unknown significance in KANSL1 showed that these faces do not match KdVS. Our data highlight quantitative facial phenotyping not only as a powerful tool to distinguish syndromes with overlapping facial dysmorphisms but also to establish pathogenicity of variants of unknown clinical significance.

Published
2021

17. Human disease genes website series: An international, open and dynamic library for up-to-date clinical information

Author

Dingemans, A.J.M., Stremmelaar, D.E., Vissers, L.E.L.M., Jansen, S, Nabais Sá, M.J., Remortele, A.M. van, Jonis, N., Truijen, K., Ven, S. van de, Ewals, J., Verbruggen, M., Koolen, D.A., Brunner, H.G., Eichler, E.E., Gecz, J., Vries, B.B.A. de, Dingemans, A.J.M., Stremmelaar, D.E., Vissers, L.E.L.M., Jansen, S, Nabais Sá, M.J., Remortele, A.M. van, Jonis, N., Truijen, K., Ven, S. van de, Ewals, J., Verbruggen, M., Koolen, D.A., Brunner, H.G., Eichler, E.E., Gecz, J., and Vries, B.B.A. de

Abstract

Contains fulltext : 231730.pdf (Publisher’s version ) (Open Access)

Published
2021

18. 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

19. Comprehensive study of 28 individuals with SIN3A-related disorder underscoring the associated mild cognitive and distinctive facial phenotype

Author

Balasubramanian, M. (Meena), Dingemans, A.J.M. (Alexander J. M.), Albaba, S. (Shadi), Richardson, R. (Ruth), Yates, T.M. (Thabo M.), Cox, H. (H.), Douzgou, S. (Sofia), Armstrong, R. (Ruth), Sansbury, F.H. (Francis H.), Burke, K.B. (Katherine B.), Fry, A.E. (Andrew E.), Ragge, N. (Nicola), Sharif, S. (Saba), Foster, A. (Alison), Sandre-Giovannoli, A. (Annachiara) de, Elouej, S. (Sahar), Vasudevan, P. (Pradeep), Mansour, S. (Sahar), Wilson, K. (Kate), Stewart, H. (Helen), Heide, S. (Solveig), Nava, C. (Caroline), Keren, B. (Boris), Demirdas, S. (Serwet), Brooks, A.S. (Alice S.), Vincent, M. (Marie), Isidor, B. (Bertrand), Küry, S. (Sebastien), Schouten, M. (Meyke), Leenders, E. (Erika), Chung, W. (Wendy), Haeringen, A. (Arie van), Scheffner, T. (Thomas), Debray, F.-G. (Francois-Guillaume), White, S.M. (Susan M.), Palafoll, M.I.V. (Maria Irene Valenzuela), Pfundt, R. (Rolph), Newbury-Ecob, R. (Ruth), Kleefstra, T. (Tjitske), Balasubramanian, M. (Meena), Dingemans, A.J.M. (Alexander J. M.), Albaba, S. (Shadi), Richardson, R. (Ruth), Yates, T.M. (Thabo M.), Cox, H. (H.), Douzgou, S. (Sofia), Armstrong, R. (Ruth), Sansbury, F.H. (Francis H.), Burke, K.B. (Katherine B.), Fry, A.E. (Andrew E.), Ragge, N. (Nicola), Sharif, S. (Saba), Foster, A. (Alison), Sandre-Giovannoli, A. (Annachiara) de, Elouej, S. (Sahar), Vasudevan, P. (Pradeep), Mansour, S. (Sahar), Wilson, K. (Kate), Stewart, H. (Helen), Heide, S. (Solveig), Nava, C. (Caroline), Keren, B. (Boris), Demirdas, S. (Serwet), Brooks, A.S. (Alice S.), Vincent, M. (Marie), Isidor, B. (Bertrand), Küry, S. (Sebastien), Schouten, M. (Meyke), Leenders, E. (Erika), Chung, W. (Wendy), Haeringen, A. (Arie van), Scheffner, T. (Thomas), Debray, F.-G. (Francois-Guillaume), White, S.M. (Susan M.), Palafoll, M.I.V. (Maria Irene Valenzuela), Pfundt, R. (Rolph), Newbury-Ecob, R. (Ruth), and Kleefstra, T. (Tjitske)

Abstract

Witteveen-Kolk syndrome (OMIM 613406) is a recently defined neurodevelopmental syndrome caused by heterozygous loss-of-function variants in SIN3A. We define the clinical and neurodevelopmental phenotypes related to SIN3A-haploinsufficiency in 28 unreported patients. Patients with SIN3A variants adversely affecting protein function have mild intellectual disability, growth and feeding difficulties. Involvement of a multidisciplinary team including a geneticist, paediatrician and neurologist should be considered in managing these patients. Patients described here were identified through a combination of clinical evaluation and gene matching strategies (GeneMatcher and Decipher). All patients consented to participate in this study. Mean age of this cohort was 8.2 years (17 males, 11 females). Out of 16 patients ≥ 8 years old assessed, eight (50%) had mild intellectual disability (ID), four had moderate ID (22%), and one had severe ID (6%). Four (25%) did not have any cognitive impairment. Other neurological symptoms such as seizures (4/28) and hypotonia (12/28) were common. Behaviour problems were reported in a minority. In patients ≥2 years, three were diagnosed with Autism Spectrum Disorder (ASD) and four with Attention Deficit Hyperactivity Disorder (ADHD). We report 27 novel variants and one previously reported variant. 24 were truncating variants; three were missense variants and one large in-frame gain including exons 10–12.

Published
2021
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20. A Case Series of Familial ARID1B Variants Illustrating Variable Expression and Suggestions to Update the ACMG Criteria

Author

Sluijs, P.J. van der, Alders, M., Dingemans, A.J.M., Parbhoo, Kareesma, Bon, B.W. van, Dempsey, J.C., Vries, B.B.A. de, Maystadt, I., Santen, G.W.E., Sluijs, P.J. van der, Alders, M., Dingemans, A.J.M., Parbhoo, Kareesma, Bon, B.W. van, Dempsey, J.C., Vries, B.B.A. de, Maystadt, I., and Santen, G.W.E.

Abstract

Contains fulltext : 237017.pdf (Publisher’s version ) (Open Access)

Published
2021

21. Behavior and cognitive functioning in Witteveen-Kolk syndrome

Author

Dongen, L.C.M. van, Wingbermühle, P.A.M., Dingemans, A.J.M., Bos-Roubos, A.G., Vermeulen, K., Pop-Purceleanu, M., Kleefstra, T., Egger, J.I.M., Dongen, L.C.M. van, Wingbermühle, P.A.M., Dingemans, A.J.M., Bos-Roubos, A.G., Vermeulen, K., Pop-Purceleanu, M., Kleefstra, T., and Egger, J.I.M.

Abstract

Contains fulltext : 221392.pdf (publisher's version ) (Open Access), Witteveen-Kolk syndrome (WITKOS) is a rare neurodevelopmental disorder characterized by developmental delay/intellectual disability, facial dysmorphisms, and short stature. The syndrome is caused by loss of function of switch-insensitive 3 transcription regulator family member A (SIN3A). Regarding behavioral functioning, Autism Spectrum Disorders (ASD), obsessive-compulsive behaviors, as well as Attention-Deficit/Hyperactivity Disorder symptoms (ADHD) have been suggested. The present study explores various aspects of neurocognitive functioning in five individuals (age range 10-23) with WITKOS. Medical records and results of extensive neuropsychological assessment are used to describe developmental trajectories and neurocognitive profiles. Systematic analysis of medical records displays developmental difficulties described as ASD or ADHD in childhood, sleep problems and internalizing problems during adolescence. Results of cognitive assessments indicate profoundly disabled (n = 1), mildly disabled (n = 2), borderline (n = 1), and average (n = 1) levels of intelligence. Furthermore, results indicate weaknesses in speed of information processing/sustained attention in all participants, and difficulties in planning and maintaining overview in three participants. Furthermore, parent reports of behavioral functioning primarily suggest problems in social functioning. Implications of both cognitive problems and social-emotional vulnerabilities for counseling are discussed and supplemented with suggestions for interventions.

Published
2020

22. Opposite Modulation of RAC1 by Mutations in TRIO Is Associated with Distinct, Domain-Specific Neurodevelopmental Disorders

Author

Barbosa, Sonia, Greville-Heygate, S., Bonnet, Maxime, Godwin, Annie, Fagotto-Kaufmann, Christine, Kajava, A.V., Dingemans, A.J.M., Vries, B.B.A. de, Schmidt, S., Baralle, Diana, Barbosa, Sonia, Greville-Heygate, S., Bonnet, Maxime, Godwin, Annie, Fagotto-Kaufmann, Christine, Kajava, A.V., Dingemans, A.J.M., Vries, B.B.A. de, Schmidt, S., and Baralle, Diana

Abstract

Contains fulltext : 217385.pdf (Publisher’s version ) (Open Access)

Published
2020

23. Mutation-specific pathophysiological mechanisms define different neurodevelopmental disorders associated with SATB1 dysfunction

Author

den Hoed, J., de Boer, E., Voisin, N., Dingemans, A.J.M., Guex, N., Wiel, L., Nellaker, C., Amudhavalli, S.M., Banka, S., Bena, F.S., Ben-Zeev, B., Bonagura, V.R., Bruel, A.-L., Brunet, T., Brunner, H.G., Chew, H.B., Chrast, J., Cimbalistienė, L., Coon, H., Délot, E.C., Démurger, F., Denommé-Pichon, A.-S., Depienne, C., Donnai, D., Dyment, D.A., Elpeleg, O., Faivre, L., Gilissen, C., Granger, L., Haber, B., Hachiya, Y., Abedi, Y.H., Hanebeck, J., Hehir-Kwa, J.Y., Horist, B., Itai, T., Jackson, A., Jewell, R., Jones, K.L., Joss, S., Kashii, H., Kato, M., Kattentidt-Mouravieva, A.A., Kok, F., Kotzaeridou, U., Krishnamurthy, V., Kučinskas, V., Kuechler, A., Lavillaureix, A., Liu, P., Manwaring, L., Matsumoto, N., Mazel, B., McWalter, K., Meiner, V., Mikati, M.A., Miyatake, S., Mizuguchi, T., Moey, L.H., Mohammed, S., Mor-Shaked, H., Mountford, H., Newbury-Ecob, R., Odent, S., Orec, L., Osmond, M., Palculict, T.B., Parker, M., Petersen, A., Pfundt, R., Preikšaitienė, E., Radtke, K., Ranza, E., Rosenfeld, J.A., Santiago-Sim, T., Schwager, C., Sinnema, M., Blok, L.S., Spillmann, R.C., Stegmann, A.P.A., Thiffault, I., Tran, L., Vaknin-Dembinsky, A., Vedovato-dos-Santos, J.H., Vergano, S.A., Vilain, E., Vitobello, A., Wagner, M., Waheeb, A., Willing, M., Zuccarelli, B., Kini, U., Newbury, D.F., Kleefstra, T., Reymond, A., Fisher, S.E., Vissers, L.E.L.M., den Hoed, J., de Boer, E., Voisin, N., Dingemans, A.J.M., Guex, N., Wiel, L., Nellaker, C., Amudhavalli, S.M., Banka, S., Bena, F.S., Ben-Zeev, B., Bonagura, V.R., Bruel, A.-L., Brunet, T., Brunner, H.G., Chew, H.B., Chrast, J., Cimbalistienė, L., Coon, H., Délot, E.C., Démurger, F., Denommé-Pichon, A.-S., Depienne, C., Donnai, D., Dyment, D.A., Elpeleg, O., Faivre, L., Gilissen, C., Granger, L., Haber, B., Hachiya, Y., Abedi, Y.H., Hanebeck, J., Hehir-Kwa, J.Y., Horist, B., Itai, T., Jackson, A., Jewell, R., Jones, K.L., Joss, S., Kashii, H., Kato, M., Kattentidt-Mouravieva, A.A., Kok, F., Kotzaeridou, U., Krishnamurthy, V., Kučinskas, V., Kuechler, A., Lavillaureix, A., Liu, P., Manwaring, L., Matsumoto, N., Mazel, B., McWalter, K., Meiner, V., Mikati, M.A., Miyatake, S., Mizuguchi, T., Moey, L.H., Mohammed, S., Mor-Shaked, H., Mountford, H., Newbury-Ecob, R., Odent, S., Orec, L., Osmond, M., Palculict, T.B., Parker, M., Petersen, A., Pfundt, R., Preikšaitienė, E., Radtke, K., Ranza, E., Rosenfeld, J.A., Santiago-Sim, T., Schwager, C., Sinnema, M., Blok, L.S., Spillmann, R.C., Stegmann, A.P.A., Thiffault, I., Tran, L., Vaknin-Dembinsky, A., Vedovato-dos-Santos, J.H., Vergano, S.A., Vilain, E., Vitobello, A., Wagner, M., Waheeb, A., Willing, M., Zuccarelli, B., Kini, U., Newbury, D.F., Kleefstra, T., Reymond, A., Fisher, S.E., and Vissers, L.E.L.M.

Abstract

Whereas large-scale statistical analyses can robustly identify disease-gene relationships, they do not accurately capture genotype-phenotype correlations or disease mechanisms. We use multiple lines of independent evidence to show that different variant types in a single gene, SATB1, cause clinically overlapping but distinct neurodevelopmental disorders. Clinical evaluation of 42 individuals carrying SATB1 variants identified overt genotype-phenotype relationships, associated with different pathophysiological mechanisms, established by functional assays. Missense variants in the CUT1 and CUT2 DNA-binding domains result in stronger chromatin binding, increased transcriptional repression and a severe phenotype. In contrast, variants predicted to result in haploinsufficiency are associated with a milder clinical presentation. A similarly mild phenotype is observed for individuals with premature protein truncating variants that escape nonsense-mediated decay, which are transcriptionally active but mislocalized in the cell. Our results suggest that in-depth mutation-specific genotype-phenotype studies are essential to capture full disease complexity and to explain phenotypic variability.

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