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1. The predictive ability of the 313 variant-based polygenic risk score for contralateral breast cancer risk prediction in women of European ancestry with a heterozygous BRCA1 or BRCA2 pathogenic variant.

Author

Lakeman, Inge MM, van den Broek, Alexandra J, Vos, Juliën AM, Barnes, Daniel R, Adlard, Julian, Andrulis, Irene L, Arason, Adalgeir, Arnold, Norbert, Arun, Banu K, Balmaña, Judith, Barrowdale, Daniel, Benitez, Javier, Borg, Ake, Caldés, Trinidad, Caligo, Maria A, Chung, Wendy K, Claes, Kathleen BM, GEMO Study Collaborators, EMBRACE Collaborators, Collée, J Margriet, Couch, Fergus J, Daly, Mary B, Dennis, Joe, Dhawan, Mallika, Domchek, Susan M, Eeles, Ros, Engel, Christoph, Evans, D Gareth, Feliubadaló, Lidia, Foretova, Lenka, Friedman, Eitan, Frost, Debra, Ganz, Patricia A, Garber, Judy, Gayther, Simon A, Gerdes, Anne-Marie, Godwin, Andrew K, Goldgar, David E, Hahnen, Eric, Hake, Christopher R, Hamann, Ute, Hogervorst, Frans BL, Hooning, Maartje J, Hopper, John L, Hulick, Peter J, Imyanitov, Evgeny N, OCGN Investigators, HEBON Investigators, KconFab Investigators, Isaacs, Claudine, Izatt, Louise, Jakubowska, Anna, James, Paul A, Janavicius, Ramunas, Jensen, Uffe Birk, Jiao, Yue, John, Esther M, Joseph, Vijai, Karlan, Beth Y, Kets, Carolien M, Konstantopoulou, Irene, Kwong, Ava, Legrand, Clémentine, Leslie, Goska, Lesueur, Fabienne, Loud, Jennifer T, Lubiński, Jan, Manoukian, Siranoush, McGuffog, Lesley, Miller, Austin, Gomes, Denise Molina, Montagna, Marco, Mouret-Fourme, Emmanuelle, Nathanson, Katherine L, Neuhausen, Susan L, Nevanlinna, Heli, Yie, Joanne Ngeow Yuen, Olah, Edith, Olopade, Olufunmilayo I, Park, Sue K, Parsons, Michael T, Peterlongo, Paolo, Piedmonte, Marion, Radice, Paolo, Rantala, Johanna, Rennert, Gad, Risch, Harvey A, Schmutzler, Rita K, Sharma, Priyanka, Simard, Jacques, Singer, Christian F, Stadler, Zsofia, Stoppa-Lyonnet, Dominique, Sutter, Christian, Tan, Yen Yen, Teixeira, Manuel R, Teo, Soo Hwang, Teulé, Alex, Thomassen, Mads, and Thull, Darcy L

Subjects
GEMO Study Collaborators, EMBRACE Collaborators, OCGN Investigators, HEBON Investigators, KconFab Investigators, Humans, Breast Neoplasms, Genetic Predisposition to Disease, BRCA1 Protein, BRCA2 Protein, Risk Factors, Retrospective Studies, Heterozygote, Mutation, Adult, Female, Prevention, Cancer, Aging, Breast Cancer, 2.1 Biological and endogenous factors, Genetics & Heredity, Genetics, Clinical Sciences
Abstract

PurposeTo evaluate the association between a previously published 313 variant-based breast cancer (BC) polygenic risk score (PRS313) and contralateral breast cancer (CBC) risk, in BRCA1 and BRCA2 pathogenic variant heterozygotes.MethodsWe included women of European ancestry with a prevalent first primary invasive BC (BRCA1 = 6,591 with 1,402 prevalent CBC cases; BRCA2 = 4,208 with 647 prevalent CBC cases) from the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), a large international retrospective series. Cox regression analysis was performed to assess the association between overall and ER-specific PRS313 and CBC risk.ResultsFor BRCA1 heterozygotes the estrogen receptor (ER)-negative PRS313 showed the largest association with CBC risk, hazard ratio (HR) per SD = 1.12, 95% confidence interval (CI) (1.06-1.18), C-index = 0.53; for BRCA2 heterozygotes, this was the ER-positive PRS313, HR = 1.15, 95% CI (1.07-1.25), C-index = 0.57. Adjusting for family history, age at diagnosis, treatment, or pathological characteristics for the first BC did not change association effect sizes. For women developing first BC

Published
2021

2. KAT6A Syndrome: genotype–phenotype correlation in 76 patients with pathogenic KAT6A variants

Author

Kennedy, Joanna, Goudie, David, Blair, Edward, Chandler, Kate, Joss, Shelagh, McKay, Victoria, Green, Andrew, Armstrong, Ruth, Lees, Melissa, Kamien, Benjamin, Hopper, Bruce, Tan, Tiong Yang, Yap, Patrick, Stark, Zornitza, Okamoto, Nobuhiko, Miyake, Noriko, Matsumoto, Naomichi, Macnamara, Ellen, Murphy, Jennifer L, McCormick, Elizabeth, Hakonarson, Hakon, Falk, Marni J, Li, Dong, Blackburn, Patrick, Klee, Eric, Babovic-Vuksanovic, Dusica, Schelley, Susan, Hudgins, Louanne, Kant, Sarina, Isidor, Bertrand, Cogne, Benjamin, Bradbury, Kimberley, Williams, Mark, Patel, Chirag, Heussler, Helen, Duff-Farrier, Celia, Lakeman, Phillis, Scurr, Ingrid, Kini, Usha, Elting, Mariet, Reijnders, Margot, Schuurs-Hoeijmakers, Janneke, Wafik, Mohamed, Blomhoff, Anne, Ruivenkamp, Claudia AL, Nibbeling, Esther, Dingemans, Alexander JM, Douine, Emilie D, Nelson, Stanley F, Hempel, Maja, Bierhals, Tatjana, Lessel, Davor, Johannsen, Jessika, Arboleda, Valerie A, and Newbury-Ecob, Ruth

Subjects
Biological Sciences, Genetics, Prevention, Brain Disorders, Rare Diseases, Pediatric, Clinical Research, Digestive Diseases, Intellectual and Developmental Disabilities (IDD), Aetiology, 2.1 Biological and endogenous factors, Adolescent, Adult, Child, Child, Preschool, Chromosome Deletion, Developmental Disabilities, Exome, Female, Genetic Association Studies, Genotype, Histone Acetyltransferases, Humans, Infant, Intellectual Disability, Male, Microcephaly, Mutation, Phenotype, Protein Isoforms, Young Adult, genetic diagnosis, phenotypic spectrum, KAT6A syndrome, chromatin modifiers, intellectual disability, DDD Study, KAT6A syndrome, chromatin modifiers, intellectual disability, Clinical Sciences, Genetics & Heredity
Abstract

PurposePathogenic variants in KAT6A have recently been identified as a cause of syndromic developmental delay. Within 2 years, the number of patients identified with pathogenic KAT6A variants has rapidly expanded and the full extent and variability of the clinical phenotype has not been reported.MethodsWe obtained data for patients with KAT6A pathogenic variants through three sources: treating clinicians, an online family survey distributed through social media, and a literature review.ResultsWe identified 52 unreported cases, bringing the total number of published cases to 76. Our results expand the genotypic spectrum of pathogenic variants to include missense and splicing mutations. We functionally validated a pathogenic splice-site variant and identified a likely hotspot location for de novo missense variants. The majority of clinical features in KAT6A syndrome have highly variable penetrance. For core features such as intellectual disability, speech delay, microcephaly, cardiac anomalies, and gastrointestinal complications, genotype- phenotype correlations show that late-truncating pathogenic variants (exons 16-17) are significantly more prevalent. We highlight novel associations, including an increased risk of gastrointestinal obstruction.ConclusionOur data expand the genotypic and phenotypic spectrum for individuals with genetic pathogenic variants in KAT6A and we outline appropriate clinical management.

Published
2019

3. NFIB Haploinsufficiency Is Associated with Intellectual Disability and Macrocephaly

Author

Schanze, Ina, Bunt, Jens, Lim, Jonathan WC, Schanze, Denny, Dean, Ryan J, Alders, Marielle, Blanchet, Patricia, Attié-Bitach, Tania, Berland, Siren, Boogert, Steven, Boppudi, Sangamitra, Bridges, Caitlin J, Cho, Megan T, Dobyns, William B, Donnai, Dian, Douglas, Jessica, Earl, Dawn L, Edwards, Timothy J, Faivre, Laurence, Fregeau, Brieana, Genevieve, David, Gérard, Marion, Gatinois, Vincent, Holder-Espinasse, Muriel, Huth, Samuel F, Izumi, Kosuke, Kerr, Bronwyn, Lacaze, Elodie, Lakeman, Phillis, Mahida, Sonal, Mirzaa, Ghayda M, Morgan, Sian M, Nowak, Catherine, Peeters, Hilde, Petit, Florence, Pilz, Daniela T, Puechberty, Jacques, Reinstein, Eyal, Rivière, Jean-Baptiste, Santani, Avni B, Schneider, Anouck, Sherr, Elliott H, Smith-Hicks, Constance, Wieland, Ilse, Zackai, Elaine, Zhao, Xiaonan, Gronostajski, Richard M, Zenker, Martin, and Richards, Linda J

Subjects
Biomedical and Clinical Sciences, Mental Health, Pediatric, Intellectual and Developmental Disabilities (IDD), Neurosciences, Rare Diseases, Behavioral and Social Science, Genetics, Brain Disorders, Aetiology, 2.1 Biological and endogenous factors, Mental health, Neurological, Adolescent, Adult, Animals, Cerebral Cortex, Child, Child, Preschool, Codon, Nonsense, Cohort Studies, Corpus Callosum, Female, Haploinsufficiency, Humans, Intellectual Disability, Male, Megalencephaly, Mice, Mice, Knockout, NFI Transcription Factors, Polymorphism, Single Nucleotide, Young Adult, NFIB, agenesis of the corpus callosum, chromosome 9p22.3, chromosome 9p23, developmental delay, haploinsufficiency, intellectual disability, macrocephaly, megalencephaly, nuclear factor I, Biological Sciences, Medical and Health Sciences, Genetics & Heredity, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

The nuclear factor I (NFI) family of transcription factors play an important role in normal development of multiple organs. Three NFI family members are highly expressed in the brain, and deletions or sequence variants in two of these, NFIA and NFIX, have been associated with intellectual disability (ID) and brain malformations. NFIB, however, has not previously been implicated in human disease. Here, we present a cohort of 18 individuals with mild ID and behavioral issues who are haploinsufficient for NFIB. Ten individuals harbored overlapping microdeletions of the chromosomal 9p23-p22.2 region, ranging in size from 225 kb to 4.3 Mb. Five additional subjects had point sequence variations creating a premature termination codon, and three subjects harbored single-nucleotide variations resulting in an inactive protein as determined using an in vitro reporter assay. All individuals presented with additional variable neurodevelopmental phenotypes, including muscular hypotonia, motor and speech delay, attention deficit disorder, autism spectrum disorder, and behavioral abnormalities. While structural brain anomalies, including dysgenesis of corpus callosum, were variable, individuals most frequently presented with macrocephaly. To determine whether macrocephaly could be a functional consequence of NFIB disruption, we analyzed a cortex-specific Nfib conditional knockout mouse model, which is postnatally viable. Utilizing magnetic resonance imaging and histology, we demonstrate that Nfib conditional knockout mice have enlargement of the cerebral cortex but preservation of overall brain structure and interhemispheric connectivity. Based on our findings, we propose that haploinsufficiency of NFIB causes ID with macrocephaly.

Published
2018

4. De Novo and Inherited Loss-of-Function Variants in TLK2: Clinical and Genotype-Phenotype Evaluation of a Distinct Neurodevelopmental Disorder

Author

Reijnders, Margot RF, Miller, Kerry A, Alvi, Mohsan, Goos, Jacqueline AC, Lees, Melissa M, de Burca, Anna, Henderson, Alex, Kraus, Alison, Mikat, Barbara, de Vries, Bert BA, Isidor, Bertrand, Kerr, Bronwyn, Marcelis, Carlo, Schluth-Bolard, Caroline, Deshpande, Charu, Ruivenkamp, Claudia AL, Wieczorek, Dagmar, Study, The Deciphering Developmental Disorders, Baralle, Diana, Blair, Edward M, Engels, Hartmut, Lüdecke, Hermann-Josef, Eason, Jacqueline, Santen, Gijs WE, Clayton-Smith, Jill, Chandler, Kate, Tatton-Brown, Katrina, Payne, Katelyn, Helbig, Katherine, Radtke, Kelly, Nugent, Kimberly M, Cremer, Kirsten, Strom, Tim M, Bird, Lynne M, Sinnema, Margje, Bitner-Glindzicz, Maria, van Dooren, Marieke F, Alders, Marielle, Koopmans, Marije, Brick, Lauren, Kozenko, Mariya, Harline, Megan L, Klaassens, Merel, Steinraths, Michelle, Cooper, Nicola S, Edery, Patrick, Yap, Patrick, Terhal, Paulien A, van der Spek, Peter J, Lakeman, Phillis, Taylor, Rachel L, Littlejohn, Rebecca O, Pfundt, Rolph, Mercimek-Andrews, Saadet, Stegmann, Alexander PA, Kant, Sarina G, McLean, Scott, Joss, Shelagh, Swagemakers, Sigrid MA, Douzgou, Sofia, Wall, Steven A, Küry, Sébastien, Calpena, Eduardo, Koelling, Nils, McGowan, Simon J, Twigg, Stephen RF, Mathijssen, Irene MJ, Nellaker, Christoffer, Brunner, Han G, and Wilkie, Andrew OM

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Genetics, Biotechnology, Brain Disorders, Human Genome, Neurosciences, Clinical Research, Aetiology, 2.1 Biological and endogenous factors, Adolescent, Adult, Base Sequence, Cell Line, Child, Child, Preschool, Facies, Female, Genetic Association Studies, Humans, Infant, Inheritance Patterns, Loss of Function Mutation, Male, Neurodevelopmental Disorders, Protein Kinases, RNA, Messenger, Translocation, Genetic, Young Adult, Deciphering Developmental Disorders Study, Tousled-like, facial averaging, haploinsufficiency, intellectual disability, kinase, Medical and Health Sciences, Genetics & Heredity, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Next-generation sequencing is a powerful tool for the discovery of genes related to neurodevelopmental disorders (NDDs). Here, we report the identification of a distinct syndrome due to de novo or inherited heterozygous mutations in Tousled-like kinase 2 (TLK2) in 38 unrelated individuals and two affected mothers, using whole-exome and whole-genome sequencing technologies, matchmaker databases, and international collaborations. Affected individuals had a consistent phenotype, characterized by mild-borderline neurodevelopmental delay (86%), behavioral disorders (68%), severe gastro-intestinal problems (63%), and facial dysmorphism including blepharophimosis (82%), telecanthus (74%), prominent nasal bridge (68%), broad nasal tip (66%), thin vermilion of the upper lip (62%), and upslanting palpebral fissures (55%). Analysis of cell lines from three affected individuals showed that mutations act through a loss-of-function mechanism in at least two case subjects. Genotype-phenotype analysis and comparison of computationally modeled faces showed that phenotypes of these and other individuals with loss-of-function variants significantly overlapped with phenotypes of individuals with other variant types (missense and C-terminal truncating). This suggests that haploinsufficiency of TLK2 is the most likely underlying disease mechanism, leading to a consistent neurodevelopmental phenotype. This work illustrates the power of international data sharing, by the identification of 40 individuals from 26 different centers in 7 different countries, allowing the identification, clinical delineation, and genotype-phenotype evaluation of a distinct NDD caused by mutations in TLK2.

Published
2018

5. Recessive Mutations in SLC38A8 Cause Foveal Hypoplasia and Optic Nerve Misrouting without Albinism

Author

Poulter, James A, Al-Araimi, Musallam, Conte, Ivan, van Genderen, Maria M, Sheridan, Eamonn, Carr, Ian M, Parry, David A, Shires, Mike, Carrella, Sabrina, Bradbury, John, Khan, Kamron, Lakeman, Phillis, Sergouniotis, Panagiotis I, Webster, Andrew R, Moore, Anthony T, Pal, Bishwanath, Mohamed, Moin D, Venkataramana, Anandula, Ramprasad, Vedam, Shetty, Rohit, Saktivel, Murugan, Kumaramanickavel, Govindasamy, Tan, Alex, Mackey, David A, Hewitt, Alex W, Banfi, Sandro, Ali, Manir, Inglehearn, Chris F, and Toomes, Carmel

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Eye Disease and Disorders of Vision, Pediatric, Neurosciences, Congenital Structural Anomalies, Clinical Research, Neurodegenerative, 2.1 Biological and endogenous factors, Aetiology, Albinism, Amino Acid Transport Systems, Neutral, Animals, Child, Consanguinity, DNA Mutational Analysis, Female, Fovea Centralis, Genes, Recessive, Homozygote, Humans, Male, Mutation, Optic Nerve, Pedigree, Phenotype, Syndrome, Medical and Health Sciences, Genetics & Heredity, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Foveal hypoplasia and optic nerve misrouting are developmental defects of the visual pathway and only co-occur in connection with albinism; to date, they have only been associated with defects in the melanin-biosynthesis pathway. Here, we report that these defects can occur independently of albinism in people with recessive mutations in the putative glutamine transporter gene SLC38A8. Nine different mutations were identified in seven Asian and European families. Using morpholino-mediated ablation of Slc38a8 in medaka fish, we confirmed that pigmentation is unaffected by loss of SLC38A8. Furthermore, by undertaking an association study with SNPs at the SLC38A8 locus, we showed that common variants within this gene modestly affect foveal thickness in the general population. This study reveals a melanin-independent component underpinning the development of the visual pathway that requires a functional role for SLC38A8.

Published
2013

6. Development, behaviour and autism in individuals with SMC1A variants

Author

Mulder, P.A., Huisman, S., Landlust, A.M., Moss, J., Bader, I., Balkom, I.D.C. van, Bisgaard, A.M., Brooks, A., Cereda, A., Cinca, C., Clark, D., Cormier-Daire, V., Deardorff, M.A., Diderich, K., Elting, M., Essen, A. van, FitzPatrick, D., Gervasini, C., Gillessen-Kaesbach, G., Girisha, K.M., Hennekam, R.C., Hilhorst-Hofstee, Y., Hopman, S., Horn, D., Isrie, M., Jansen, S., Jespersgaard, C., Kaiser, F.J., Kaur, M., Kleefstra, T., Krantz, I.D., Lakeman, P., Lessel, D., Michot, C., Noon, S.E., Oliver, C., Parenti, I., Pie, J., Piening, S., Puisac, B., Ramos, F.J., Redeker, E., Rieubland, C., Russo, S., Selicorni, A., Tumer, Z., Vorstenbosch, R., Vries, I.M., Wenger, T.L., Wierzba, J., SMC1A Consortium, Clinical Genetics, Pediatric surgery, APH - Quality of Care, Human genetics, Amsterdam Reproduction & Development (AR&D), Graduate School, ANS - Cellular & Molecular Mechanisms, and Paediatric Genetics

Subjects
cognition, Male, Autism Spectrum Disorder, Chromosomal Proteins, Non-Histone, CHILDREN, Cell Cycle Proteins, COMMUNICATION, Pediatrics, 0302 clinical medicine, De Lange Syndrome, Intellectual disability, Developmental and Educational Psychology, Spectrum disorder, Child, self-injurious behaviour, 05 social sciences, SELF-INJURIOUS-BEHAVIOR, Perinatology, PREVALENCE, and Child Health, Psychiatry and Mental health, Phenotype, DE-LANGE-SYNDROME, Autism spectrum disorder, Child, Preschool, Female, Psychology, 050104 developmental & child psychology, Clinical psychology, Behavioural phenotype, Adult, Down syndrome, cornelia de lange syndrome, Cornelia de Lange Syndrome, Adolescent, autism, Rett syndrome, 03 medical and health sciences, Young Adult, All institutes and research themes of the Radboud University Medical Center, Journal Article, medicine, Humans, 0501 psychology and cognitive sciences, Cognitive Dysfunction, Pediatrics, Perinatology, and Child Health, rett syndrome, SPECTRUM DISORDER, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], MUTATIONS, Infant, NIPBL, medicine.disease, Cross-Sectional Studies, Pediatrics, Perinatology and Child Health, Autism, Down Syndrome, Self-Injurious Behavior, 030217 neurology & neurosurgery
Abstract

Introduction: Development and behaviour in Cornelia de Lange Syndrome (CdLS), including autism characteristics, have been described infrequently stratified to genetic cause and only a few studies have considered behavioural characteristics in relation to developmental level. Here, we describe the behavioural phenotype in individuals with CdLS with SMC1A variants. Methods: We performed an international, interdisciplinary study on 51 individuals with SMC1A variants. Results of questionnaire studies are compared to those in individuals with Down Syndrome and with Autism Spectrum Disorder. Results on cognition and self-injurious behaviour (SIB) are compared to those in individuals with CdLS caused by NIPBL variants. For Dutch participants with SMC1A variants we performed direct in-person assessments of cognition, autism, and added an interview and questionnaire on adaptive behaviour and sensory processing. Results: Individuals with SMC1A variants show a higher cognitive level and less SIB than individuals with NIPBL variants. Individuals with SMC1A variants without classic CdLS phenotype but with a Rett-like phenotype show more severe intellectual disability and more SIB compared to those with a CdLS phenotype. Autism is less present if outcomes in direct in-person assessments are evaluated taking developmental level into account compared to results based on a questionnaire. Conclusions: Behaviour in individuals with CdLS should be evaluated taking genetic cause into account. Detailed interdisciplinary approaches are of clinical importance to inform tailored care and may eventually improve quality of life of patients and families.

Published
2019
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7. De Novo and Inherited Loss-of-Function Variants in TLK2: Clinical and Genotype-Phenotype Evaluation of a Distinct Neurodevelopmental Disorder

Author

Reijnders, MRF, Miller, KA, Alvi, M, Goos, JAC, Lees, MM, de Burca, A, Henderson, A, Kraus, A, Mikat, B, de Vries, BBA, Isidor, B, Kerr, B, Marcelis, C, Schluth-Bolard, C, Deshpande, C, Ruivenkamp, CAL, Wieczorek, D, Deciphering Developmental Disorders Study, Baralle, D, Blair, EM, Engels, H, Lüdecke, H-J, Eason, J, Santen, GWE, Clayton-Smith, J, Chandler, K, Tatton-Brown, K, Payne, K, Helbig, K, Radtke, K, Nugent, KM, Cremer, K, Strom, TM, Bird, LM, Sinnema, M, Bitner-Glindzicz, M, van Dooren, MF, Alders, M, Koopmans, M, Brick, L, Kozenko, M, Harline, ML, Klaassens, M, Steinraths, M, Cooper, NS, Edery, P, Yap, P, Terhal, PA, van der Spek, PJ, Lakeman, P, Taylor, RL, Littlejohn, RO, Pfundt, R, Mercimek-Andrews, S, Stegmann, APA, Kant, SG, McLean, S, Joss, S, Swagemakers, SMA, Douzgou, S, Wall, SA, Küry, S, Calpena, E, Koelling, N, McGowan, SJ, Twigg, SRF, Mathijssen, IMJ, Nellaker, C, Brunner, HG, and Wilkie, AOM

Subjects
Adult, Male, Adolescent, kinase, Messenger, Inheritance Patterns, Translocation, Medical and Health Sciences, Cell Line, Young Adult, Genetic, Clinical Research, Loss of Function Mutation, Genetics, 2.1 Biological and endogenous factors, Humans, Aetiology, Child, Preschool, Genetic Association Studies, Genetics & Heredity, Tousled-like, Base Sequence, Human Genome, Neurosciences, Facies, Infant, Deciphering Developmental Disorders Study, Biological Sciences, Brain Disorders, haploinsufficiency, Neurodevelopmental Disorders, intellectual disability, RNA, Female, Protein Kinases, facial averaging, Biotechnology
Abstract

Next-generation sequencing is a powerful tool for the discovery of genes related to neurodevelopmental disorders (NDDs). Here, we report the identification of a distinct syndrome due to de novo or inherited heterozygous mutations in Tousled-like kinase 2 (TLK2) in 38 unrelated individuals and two affected mothers, using whole-exome and whole-genome sequencing technologies, matchmaker databases, and international collaborations. Affected individuals had a consistent phenotype, characterized by mild-borderline neurodevelopmental delay (86%), behavioral disorders (68%), severe gastro-intestinal problems (63%), and facial dysmorphism including blepharophimosis (82%), telecanthus (74%), prominent nasal bridge (68%), broad nasal tip (66%), thin vermilion of the upper lip (62%), and upslanting palpebral fissures (55%). Analysis of cell lines from three affected individuals showed that mutations act through a loss-of-function mechanism in at least two case subjects. Genotype-phenotype analysis and comparison of computationally modeled faces showed that phenotypes of these and other individuals with loss-of-function variants significantly overlapped with phenotypes of individuals with other variant types (missense and C-terminal truncating). This suggests that haploinsufficiency of TLK2 is the most likely underlying disease mechanism, leading to a consistent neurodevelopmental phenotype. This work illustrates the power of international data sharing, by the identification of 40 individuals from 26 different centers in 7 different countries, allowing the identification, clinical delineation, and genotype-phenotype evaluation of a distinct NDD caused by mutations in TLK2.

Published
2018

8. De Novo and Inherited Loss-of-Function Variants in TLK2 : Clinical and Genotype-Phenotype Evaluation of a Distinct Neurodevelopmental Disorder

Author

Reijnders, M.R.F., Miller, K.A., Alvi, M., Goos, J.A.C., Lees, M.M., Burca, A. de, Henderson, A., Kraus, A., Mikat, B., Vries, B.B.A. de, Isidor, B., Kerr, B., Marcelis, C.L.M., Schluth-Bolard, C., Deshpande, C., Ruivenkamp, C.A.L., Wieczorek, D., Baralle, D., Blair, E.M., Engels, H., Ludecke, H.J., Eason, J., Santen, G.W.E., Clayton-Smith, J., Chandler, K., Tatton-Brown, K., Payne, K., Helbig, K., Radtke, K., Nugent, K.M., Cremer, K., Strom, T.M., Bird, L.M., Sinnema, M., Bitner-Glindzicz, M., Dooren, M.F. van, Alders, M., Koopmans, M., Brick, L., Kozenko, M., Harline, M.L., Klaassens, M., Steinraths, M., Cooper, N.S., Edery, P., Yap, P., Terhal, P.A., Spek, P.J. van der, Lakeman, P., Taylor, R.L., Littlejohn, R.O., Pfundt, R.P., Mercimek-Andrews, S., Stegmann, A.P.A., Kant, S.G., McLean, S., Joss, S., Swagemakers, S.M.A., Douzgou, S., Wall, S.A., Kury, S., Calpena, E., Koelling, N., McGowan, S.J., Twigg, S.R.F., Mathijssen, I.M.J., Nellaker, C., Brunner, H.G., Wilkie, A.O.M., Plastic and Reconstructive Surgery and Hand Surgery, Clinical Genetics, and Pathology

Subjects
Tousled-like, Facial Averaging, Haploinsufficiency, Intellectual Disability, Kinase, Adult, Male, Adolescent, kinase, viruses, Inheritance Patterns, Medizin, Translocation, Genetic, Cell Line, Young Adult, Loss of Function Mutation, Report, Humans, RNA, Messenger, Child, Genetic Association Studies, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Base Sequence, Facies, Infant, haploinsufficiency, Neurodevelopmental Disorders, intellectual disability, Child, Preschool, Female, Protein Kinases, facial averaging, Rare cancers Radboud Institute for Health Sciences [Radboudumc 9]
Abstract

Human adenovirus (HAdV) E1B-55K is a multifunctional regulator of productive viral replication and oncogenic transformation in nonpermissive mammalian cells. These functions depend on E1B-55K's posttranslational modification with the SUMO protein and its binding to HAdV E4orf6. Both early viral proteins recruit specific host factors to form an E3 ubiquitin ligase complex that targets antiviral host substrates for proteasomal degradation. Recently, we reported that the PML-NB associated factor Daxx represses efficient HAdV productive infection and is proteasomally degraded via a SUMO-E1B-55K-dependent, E4orf6-independent pathway, the details of which remained to be established. RNF4, a cellular SUMO-targeted ubiquitin ligase (STUbL), induces ubiquitinylation of specific SUMOy lated proteins and plays an essential role during DNA repair. Here, we show that E1B-55K recruits RNF4 to the insoluble nuclear matrix fraction of the infected cell to support RNF4/Daxx association, promoting Daxx PTM and thus inhibiting this antiviral factor. Removing RNF4 from infected cells using RNA interference resulted in blocking the proper establishment of viral replication centers and significantly diminished viral gene expression. These results provide a model for how HAdV antagonize the antiviral host responses by exploiting the functional capacity of cellular STUbLs. Thus, RNF4 and its STUbL function represent a positive factor during lytic infection and a novel candidate for future therapeutic antiviral intervention strategies.IMPORTANCE Daxx is a PML-NB-associated transcription factor that was recently shown to repress efficient HAdV productive infection. To counteract this antiviral measurement during infection, Daxx is degraded via a novel pathway including viral E1B-55K and host proteasomes. This virus-mediated degradation is independent of the classical HAdV E3 ubiquitin ligase complex, which is essential during viral infection to target other host antiviral substrates. To maintain a productive viral life cycle, HAdV E1B-55K early viral protein inhibits the chromatin-remodeling factor Daxx in a SUMO-dependent manner. In addition, viral E1B-55K protein recruits the STUbL RNF4 and sequesters it into the insoluble fraction of the infected cell. E1B-55K promotes complex formation between RNF4-and E1B-55K-targeted Daxx protein, supporting Daxx posttranslational modification prior to functional inhibition. Hence, RNF4 represents a novel host factor that is beneficial for HAdV gene expression by supporting Daxx counteraction. In this regard, RNF4 and other STUbL proteins might represent novel targets for therapeutic intervention.

Published
2018

9. Implementation of preconceptional carrier screening for cystic fibrosis and haemoglobinopathies

Author

Achterbergh, R., Lakeman, P., Stemerding, D., Moors, E.H.M., Cornel, M.C., Innovation Studies, Section Innovation Studies, Innovation Studies, Section Innovation Studies, Other departments, Human genetics, and Faculty of Behavioural, Management and Social Sciences

Subjects
Male, medicine.medical_specialty, Sociotechnical system, Process management, Sociotechnical analysis, Process (engineering), Attunement, cystic fibrosis, IR-78619, Health care, Taverne, Humans, Medicine, Genetic Testing, Program Development, Structural approach, Netherlands, Gynecology, business.industry, Genetic Carrier Screening, Health Policy, Public health, Health Plan Implementation, Public health care, Hemoglobinopathies, Preconceptional, METIS-240991, Haemoglobinopathy, Implementation, Screening, Female, Preconception Care, business, Carrier screening
Abstract

Objective To obtain more insight into the process of potential implementation of a screening program, which aims to identify carriers of cystic fibrosis and haemoglobinopathies before pregnancy, in order to enable couples at high risk of having a child with these disorders, to make informed reproductive decisions. Methods Use of sociotechnical analysis, based on a model of co-evolution between technology and society, and, for comparison, the study of the implementation processes of two already existing health care programs with similar aspects to the screening program at issue. Results Factors important for success appeared to be the existence of sociotechnical niches, in which technological options can be developed and studied in an experimental setting; a structural approach of providing information to future parents; a party that can articulate demand; governmental involvement in the attunement between various stakeholders; and a screening infrastructure in which large-scale DNA diagnostic services are available. Conclusions Successful implementation of preconceptional carrier screening for cystic fibrosis and haemoglobinopathies will depend on changes at both regime and landscape level, including the establishment of a new preconceptional health care setting and a clearly visible public health authority which can coordinate, monitor and evaluate such an initiative in public health care.

Published
2007
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10. Recessive Mutations in SLC38A8 Cause Foveal Hypoplasia and Optic Nerve Misrouting without Albinism

Author

Eamonn Sheridan, Chris F. Inglehearn, Murugan Saktivel, Phillis Lakeman, Rohit Shetty, Anandula Venkataramana, Manir Ali, Sabrina Carrella, Bishwanath Pal, Ian M. Carr, Alex W. Hewitt, James A. Poulter, Maria M. van Genderen, Musallam Al-Araimi, Govindasamy Kumaramanickavel, Vedam L. Ramprasad, Mike Shires, David A. Mackey, David A. Parry, Carmel Toomes, Kamron N. Khan, Andrew R. Webster, Panagiotis I. Sergouniotis, Anthony T. Moore, Sandro Banfi, Moin Mohamed, Alex Tai Loong Tan, Ivan Conte, John Bradbury, Poulter, J. A., Al-Araimi, M., Conte, I., Van Genderen, M. M., Sheridan, E., Carr, I. M., Parry, D. A., Shires, M., Carrella, S., Bradbury, J., Khan, K., Lakeman, P., Sergouniotis, P. I., Webster, A. R., Moore, A. T., Pal, B., Mohamed, M. D., Venkataramana, A., Ramprasad, V., Shetty, R., Saktivel, M., Kumaramanickavel, G., Tan, A., Mackey, D. A., Hewitt, A. W., Banfi, S., Ali, M., Inglehearn, C. F., Toomes, C., Human Genetics, Human genetics, Other Research, Poulter, Ja, Al Araimi, M, Conte, I, van Genderen, Mm, Sheridan, E, Carr, Im, Parry, Da, Shires, M, Carrella, S, Bradbury, J, Khan, K, Lakeman, P, Sergouniotis, Pi, Webster, Ar, Moore, At, Pal, B, Mohamed, Md, Venkataramana, A, Ramprasad, V, Shetty, R, Saktivel, M, Kumaramanickavel, G, Tan, A, Mackey, Da, Hewitt, Aw, Banfi, Sandro, Ali, M, and Inglehearn, Cf

Subjects
Male, Fovea Centralis, Amino Acid Transport Systems, genetic structures, Neutral, DNA Mutational Analysis, Neurodegenerative, Medical and Health Sciences, Consanguinity, 0302 clinical medicine, Foveal, 2.1 Biological and endogenous factors, Genetics(clinical), Aetiology, Child, Genetics (clinical), Pediatric, Genetics & Heredity, Genetics, 0303 health sciences, education.field_of_study, Homozygote, Syndrome, Biological Sciences, Hypoplasia, Pedigree, Phenotype, Optic nerve, Albinism, Female, Human, Population, Single-nucleotide polymorphism, Locus (genetics), Genes, Recessive, Biology, DNA Mutational Analysi, 03 medical and health sciences, Clinical Research, medicine, Recessive, Animals, Humans, education, Eye Disease and Disorders of Vision, 030304 developmental biology, Fovea Centrali, Animal, Neurosciences, Optic Nerve, medicine.disease, eye diseases, Amino Acid Transport Systems, Neutral, Genes, Mutation, 030221 ophthalmology & optometry, Congenital Structural Anomalies, sense organs
Abstract

Foveal hypoplasia and optic nerve misrouting are developmental defects of the visual pathway and only co-occur in connection with albinism; to date, they have only been associated with defects in the melanin-biosynthesis pathway. Here, we report that these defects can occur independently of albinism in people with recessive mutations in the putative glutamine transporter gene SLC38A8. Nine different mutations were identified in seven Asian and European families. Using morpholino-mediated ablation of Slc38a8 in medaka fish, we confirmed that pigmentation is unaffected by loss of SLC38A8. Furthermore, by undertaking an association study with SNPs at the SLC38A8 locus, we showed that common variants within this gene modestly affect foveal thickness in the general population. This study reveals a melanin-independent component underpinning the development of the visual pathway that requires a functional role for SLC38A8.

Published
2013
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