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29 results on '"Brigid M, Regan"'

1. Disruptive mutations in TANC2 define a neurodevelopmental syndrome associated with psychiatric disorders

Author

Hui Guo, Elisa Bettella, Paul C. Marcogliese, Rongjuan Zhao, Jonathan C. Andrews, Tomasz J. Nowakowski, Madelyn A. Gillentine, Kendra Hoekzema, Tianyun Wang, Huidan Wu, Sharayu Jangam, Cenying Liu, Hailun Ni, Marjolein H. Willemsen, Bregje W. van Bon, Tuula Rinne, Servi J. C. Stevens, Tjitske Kleefstra, Han G. Brunner, Helger G. Yntema, Min Long, Wenjing Zhao, Zhengmao Hu, Cindy Colson, Nicolas Richard, Charles E. Schwartz, Corrado Romano, Lucia Castiglia, Maria Bottitta, Shweta U. Dhar, Deanna J. Erwin, Lisa Emrick, Boris Keren, Alexandra Afenjar, Baosheng Zhu, Bing Bai, Pawel Stankiewicz, Kristin Herman, University of Washington Center for Mendelian Genomics, Saadet Mercimek-Andrews, Jane Juusola, Amy B. Wilfert, Rami Abou Jamra, Benjamin Büttner, Heather C. Mefford, Alison M. Muir, Ingrid E. Scheffer, Brigid M. Regan, Stephen Malone, Jozef Gecz, Jan Cobben, Marjan M. Weiss, Quinten Waisfisz, Emilia K. Bijlsma, Mariëtte J. V. Hoffer, Claudia A. L. Ruivenkamp, Stefano Sartori, Fan Xia, Jill A. Rosenfeld, Raphael A. Bernier, Michael F. Wangler, Shinya Yamamoto, Kun Xia, Alexander P. A. Stegmann, Hugo J. Bellen, Alessandra Murgia, and Evan E. Eichler

Subjects
Science
Abstract

Neurodevelopmental disorders (NDDs) are a heterogeneous group of diseases for which the genetic basis is still unknown in more than half of the cases. Here, the authors report a NDD associated with disruptive variants in the TANC2 gene and show that rols, the TANC2 homolog in flies, is required for synapse growth and function.

Published
2019
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2. The diverse pleiotropic effects of spliceosomal protein <scp>PUF60</scp> : A case series of Verheij syndrome

Author

Andrew Paul Fennell, Anne Elizabeth Baxter, Samuel Frank Berkovic, Carolyn Jane Ellaway, Caitlin Forwood, Michael Stephen Hildebrand, Smitha Kumble, Colina McKeown, David Mowat, Gemma Poke, Sulekha Rajagopalan, Brigid M. Regan, Ingrid Eileen Scheffer, Zornitza Stark, Chloe Alice Stutterd, Tiong Yang Tan, Ella Jane Wilkins, Alison Yeung, and Matthew Frank Hunter

Subjects
Repressor Proteins, Phenotype, Intellectual Disability, Microcephaly, Spliceosomes, Genetics, Humans, Abnormalities, Multiple, RNA Splicing Factors, Genetics (clinical)
Abstract

Verheij syndrome (VRJS) is a rare craniofacial spliceosomopathy presenting with craniofacial dysmorphism, multiple congenital anomalies and variable neurodevelopmental delay. It is caused by single nucleotide variants (SNVs) in PUF60 or interstitial deletions of the 8q24.3 region. PUF60 encodes a splicing factor which forms part of the spliceosome. To date, 36 patients with a sole diagnosis of VRJS due to disease-causing PUF60 SNVs have been reported in peer-reviewed publications. Although the depth of their phenotyping has varied greatly, they exhibit marked phenotypic heterogeneity. We report 10 additional unrelated patients, including the first described patients of Khmer, Indian, and Vietnamese ethnicities, and the eldest patient to date, with 10 heterozygous PUF60 variants identified through exome sequencing, 8 previously unreported. All patients underwent deep phenotyping identifying variable dysmorphism, growth delay, neurodevelopmental delay, and multiple congenital anomalies, including several unique features. The eldest patient is the only reported individual with a germline variant and neither neurodevelopmental delay nor intellectual disability. In combining these detailed phenotypic data with that of previously reported patients (n = 46), we further refine the known frequencies of features associated with VRJS. These include neurodevelopmental delay/intellectual disability (98%), axial skeletal anomalies (74%), appendicular skeletal anomalies (73%), oral anomalies (68%), short stature (66%), cardiac anomalies (63%), brain malformations (48%), hearing loss (46%), microcephaly (41%), colobomata (38%), and other ocular anomalies (65%). This case series, incorporating three patients from previously unreported ethnic backgrounds, further delineates the broad pleiotropy and mutational spectrum of PUF60 pathogenic variants.

Published
2022
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3. Integrated in silico and experimental assessment of disease relevance of PCDH19 missense variants

Author

Stuart M. Pitson, Mark A. Corbett, Stephen P. Robertson, Rebekah de Nys, Heidi E. Kirsch, Deepak Gill, Melissa R. Pitman, Samuel F. Berkovic, Benjamin J. Halliday, Lachlan A. Jolly, Slavé Petrovski, Jozef Gecz, Kavitha Kothur, Kristy L. Kolc, Brigid M. Regan, Alison Gardner, Duyen H. Pham, Ingrid E. Scheffer, Sulekha Rajagopalan, Raman Kumar, Renèe B. Schulz, Sarah E. Heron, Pham, Duyen H, Pitman, Melissa R, Kumar, Raman, Jolly, Lachlan A, Pitson, Stuart M, and Gecz, Jozef

Subjects
medicine.medical_specialty, PCDH19, In silico, Mutation, Missense, Protocadherin, Disease, Computational biology, Biology, functional test, variant assessment, 03 medical and health sciences, Genetics, medicine, Humans, Missense mutation, Relevance (information retrieval), Genetics (clinical), 030304 developmental biology, 0303 health sciences, Epilepsy, Molecular pathology, 030305 genetics & heredity, Sequence Analysis, DNA, Cadherins, Protocadherins, VUS, epilepsy, Medical genetics, Function (biology)
Abstract

PCDH19 is a nonclustered protocadherin molecule involved in axon bundling, synapse function, and transcriptional coregulation. Pathogenic variants in PCDH19 cause infantile-onset epilepsy known as PCDH19-clustering epilepsy or PCDH19-CE. Recent advances in DNA-sequencing technologies have led to a significant increase in the number of reported PCDH19-CE variants, many of uncertain significance. We aimed to determine the best approaches for assessing the disease relevance of missense variants in PCDH19. The application of the American College of Medical Genetics and Association for Molecular Pathology (ACMG-AMP) guidelines was only 50% accurate. Using a training set of 322 known benign or pathogenic missense variants, we identified MutPred2, MutationAssessor, and GPP as the best performing in silico tools. We generated a protein structural model of the extracellular domain and assessed 24 missense variants. We also assessed 24 variants using an in vitro reporter assay. A combination of these tools was 93% accurate in assessing known pathogenic and benign PCDH19 variants. We increased the accuracy of the ACMG-AMP classification of 45 PCDH19 variants from 50% to 94%, using these tools. In summary, we have developed a robust toolbox for the assessment of PCDH19 variant pathogenicity to improve the accuracy of PCDH19-CE variant classification. Refereed/Peer-reviewed

Published
2021
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4. Familial adult myoclonic epilepsy type 1 SAMD12 TTTCA repeat expansion arose 17,000 years ago and is present in Sri Lankan and Indian families

Author

Susannah T. Bellows, Jozef Gecz, Matthew Coleman, Thessa Kroes, Amy L Schneider, Brigid M. Regan, Karen Oliver, Samuel F. Berkovic, Haloom Rafehi, Douglas E. Crompton, Mark F. Bennett, Mark A. Corbett, Melanie Bahlo, Neblina Sikta, Michael S. Hildebrand, and Ingrid E. Scheffer

Subjects
Male, Indian origin, India, Epilepsies, Myoclonic, Nerve Tissue Proteins, Locus (genetics), Biology, Brief Communication, Genetics, medicine, Humans, Genetics (clinical), Sri Lanka, Whole genome sequencing, Haplotype, medicine.disease, Founder Effect, Pedigree, Haplotypes, Evolutionary biology, Mutation, Myoclonic epilepsy, Female, Sri lanka, Trinucleotide repeat expansion, Founder effect
Abstract

Familial adult myoclonic epilepsy 1 (FAME1), first recognised in Japanese families, was recently shown to be caused by a TTTCA repeat insertion in intron 4 of SAMD12 on chromosome 8. We performed whole genome sequencing on two families with FAME, one of Sri Lankan origin and the other of Indian origin, and identified a TTTCA repeat insertion in SAMD12 in both families. Haplotype analysis revealed that both families shared the same core ancestral haplotype reported in Japanese and Chinese families with FAME1. Mutation dating, based on the length of shared haplotypes, estimated the age of the ancestral haplotype to be ~670 generations, or 17,000 years old. Our data extend the geographic range of this repeat expansion to Southern Asia and potentially implicate an even broader regional distribution given the age of the variant. This finding suggests patients of Asian ancestry with suspected FAME should be screened for the SAMD12 TTTCA expansion.

Published
2020
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5. Development and Validation of a Prediction Model for Early Diagnosis of SCN1A-Related Epilepsies

Author

Andreas Brunklaus, Eduardo Pérez-Palma, Ismael Ghanty, Ji Xinge, Eva Brilstra, Berten Ceulemans, Nicole Chemaly, Iris de Lange, Christel Depienne, Renzo Guerrini, Davide Mei, Rikke S. Møller, Rima Nabbout, Brigid M. Regan, Amy L. Schneider, Ingrid E. Scheffer, An-Sofie Schoonjans, Joseph D. Symonds, Sarah Weckhuysen, Michael W. Kattan, Sameer M. Zuberi, and Dennis Lal

Subjects
Epilepsy, NAV1.1 Voltage-Gated Sodium Channel/genetics, Epilepsies, Myoclonic/diagnosis, Medizin, Epilepsies, Myoclonic, NAV1.1 Voltage-Gated Sodium Channel, Cohort Studies, Early Diagnosis, Mutation, Humans, Neurology (clinical), Human medicine, Epilepsy/diagnosis, Child, Research Article, Retrospective Studies
Abstract

Background and ObjectivesPathogenic variants in the neuronal sodium channel α1 subunit gene (SCN1A) are the most frequent monogenic cause of epilepsy. Phenotypes comprise a wide clinical spectrum, including severe childhood epilepsy; Dravet syndrome, characterized by drug-resistant seizures, intellectual disability, and high mortality; and the milder genetic epilepsy with febrile seizures plus (GEFS+), characterized by normal cognition. Early recognition of a child's risk for developing Dravet syndrome vs GEFS+ is key for implementing disease-modifying therapies when available before cognitive impairment emerges. Our objective was to develop and validate a prediction model using clinical and genetic biomarkers for early diagnosis of SCN1A-related epilepsies.MethodsWe performed a retrospective multicenter cohort study comprising data from patients with SCN1A-positive Dravet syndrome and patients with GEFS+ consecutively referred for genetic testing (March 2001–June 2020) including age at seizure onset and a newly developed SCN1A genetic score. A training cohort was used to develop multiple prediction models that were validated using 2 independent blinded cohorts. Primary outcome was the discriminative accuracy of the model predicting Dravet syndrome vs other GEFS+ phenotypes.ResultsA total of 1,018 participants were included. The frequency of Dravet syndrome was 616/743 (83%) in the training cohort, 147/203 (72%) in validation cohort 1, and 60/72 (83%) in validation cohort 2. A high SCN1A genetic score (133.4 [SD 78.5] vs 52.0 [SD 57.5]; p < 0.001) and young age at onset (6.0 [SD 3.0] vs 14.8 [SD 11.8] months; p < 0.001) were each associated with Dravet syndrome vs GEFS+. A combined SCN1A genetic score and seizure onset model separated Dravet syndrome from GEFS+ more effectively (area under the curve [AUC] 0.89 [95% CI 0.86–0.92]) and outperformed all other models (AUC 0.79–0.85; p < 0.001). Model performance was replicated in both validation cohorts 1 (AUC 0.94 [95% CI 0.91–0.97]) and 2 (AUC 0.92 [95% CI 0.82–1.00]).DiscussionThe prediction model allows objective estimation at disease onset whether a child will develop Dravet syndrome vs GEFS+, assisting clinicians with prognostic counseling and decisions on early institution of precision therapies (http://scn1a-prediction-model.broadinstitute.org/).Classification of EvidenceThis study provides Class II evidence that a combined SCN1A genetic score and seizure onset model distinguishes Dravet syndrome from other GEFS+ phenotypes.

Published
2022
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6. Association of SLC32A1 Missense Variants With Genetic Epilepsy With Febrile Seizures Plus

Author

Samuel F. Berkovic, Jozef Gecz, Michael R. Sperling, Peter Widdess-Walsh, Rebekah V. Harris, Mark A. Corbett, Michael S. Hildebrand, Erin L. Heinzen, James T. Pelekanos, Sarah E. Heron, Melanie Bahlo, Katherine L. Helbig, Matthew Coleman, Brigid M. Regan, Ingrid E. Scheffer, Alison Gardner, Slavé Petrovski, Mark F. Bennett, Bronwyn E. Grinton, Sheryl R. Haut, and Eric B. Geller

Subjects
Male, 0301 basic medicine, Vesicular Inhibitory Amino Acid Transport Proteins, Mutation, Missense, Biology, Seizures, Febrile, Article, Idiopathic generalized epilepsy, 03 medical and health sciences, symbols.namesake, Epilepsy, 0302 clinical medicine, medicine, Humans, Missense mutation, Generalized epilepsy, Gene, Genetic Association Studies, Exome sequencing, Genetics, Whole genome sequencing, Sanger sequencing, Genetic Variation, medicine.disease, Pedigree, 030104 developmental biology, symbols, Epilepsy, Generalized, Female, Neurology (clinical), 030217 neurology & neurosurgery
Abstract

ObjectiveTo identify the causative gene in a large unsolved family with genetic epilepsy with febrile seizures plus (GEFS+), we sequenced the genomes of family members, and then determined the contribution of the identified gene to the pathogenicity of epilepsies by examining sequencing data from 2,772 additional patients.MethodsWe performed whole genome sequencing of 3 members of a GEFS+ family. Subsequently, whole exome sequencing data from 1,165 patients with epilepsy from the Epi4K dataset and 1,329 Australian patients with epilepsy from the Epi25 dataset were interrogated. Targeted resequencing was performed on 278 patients with febrile seizures or GEFS+ phenotypes. Variants were validated and familial segregation examined by Sanger sequencing.ResultsEight previously unreported missense variants were identified in SLC32A1, coding for the vesicular inhibitory amino acid cotransporter VGAT. Two variants cosegregated with the phenotype in 2 large GEFS+ families containing 8 and 10 affected individuals, respectively. Six further variants were identified in smaller families with GEFS+ or idiopathic generalized epilepsy (IGE).ConclusionMissense variants in SLC32A1 cause GEFS+ and IGE. These variants are predicted to alter γ-aminobutyric acid (GABA) transport into synaptic vesicles, leading to altered neuronal inhibition. Examination of further epilepsy cohorts will determine the full genotype–phenotype spectrum associated with SLC32A1 variants.

Published
2021

7. Distinct gene-set burden patterns underlie common generalized and focal epilepsies

Author

Mahmoud Koko, Roland Krause, Thomas Sander, Dheeraj Reddy Bobbili, Michael Nothnagel, Patrick May, Holger Lerche, Yen-Chen Anne Feng, Daniel P Howrigan, Liam E Abbott, Katherine Tashman, Felecia Cerrato, Tarjinder Singh, Henrike Heyne, Andrea Byrnes, Claire Churchhouse, Nick Watts, Matthew Solomonson, Dennis Lal, Erin L Heinzen, Ryan S Dhindsa, Kate E Stanley, Gianpiero L Cavalleri, Hakon Hakonarson, Ingo Helbig, Sarah Weckhuysen, Slavé Petrovski, Sitharthan Kamalakaran, Sanjay M Sisodiya, Patrick Cossette, Chris Cotsapas, Peter DeJonghe, Tracy Dixon-Salazar, Renzo Guerrini, Patrick Kwan, Anthony G Marson, Randy Stewart, Chantal Depondt, Dennis J Dlugos, Ingrid E Scheffer, Pasquale Striano, Catharine Freyer, Kevin McKenna, Brigid M Regan, Susannah T Bellows, Costin Leu, Caitlin A Bennett, Esther M C Johns, Alexandra Macdonald, Hannah Shilling, Rosemary Burgess, Dorien Weckhuysen, Melanie Bahlo, Terence J O'Brien, Marian Todaro, Hannah Stamberger, Danielle M Andrade, Tara R Sadoway, Kelly Mo, Heinz Krestel, Sabina Gallati, Savvas S Papacostas, Ioanna Kousiappa, George A Tanteles, Katalin Štěrbová, Markéta Vlčková, Lucie Sedláčková, Petra Laššuthová, Karl Martin Klein, Felix Rosenow, Philipp S Reif, Susanne Knake, Wolfram S Kunz, Gábor Zsurka, Christian E Elger, Jürgen Bauer, Michael Rademacher, Manuela Pendziwiat, Hiltrud Muhle, Annika Rademacher, Andreas vanBaalen, Sarah vonSpiczak, Ulrich Stephani, Zaid Afawi, Amos D Korczyn, Moien Kanaan, Christina Canavati, Gerhard Kurlemann, Karen Müller-Schlüter, Gerhard Kluger, Martin Häusler, Ilan Blatt, Johannes R Lemke, Ilona Krey, Yvonne G Weber, Stefan Wolking, Felicitas Becker, Christian Hengsbach, Sarah Rau, Ana F Maisch, Bernhard J Steinhoff, Andreas Schulze-Bonhage, Susanne Schubert-Bast, Herbert Schreiber, Ingo Borggräfe, Christoph J Schankin, Thomas Mayer, Rudolf Korinthenberg, Knut Brockmann, Dieter Dennig, Rene Madeleyn, Reetta Kälviäinen, Pia Auvinen, Anni Saarela, Tarja Linnankivi, Anna-Elina Lehesjoki, Mark I Rees, Seo-Kyung Chung, William O Pickrell, Robert Powell, Natascha Schneider, Simona Balestrini, Sara Zagaglia, Vera Braatz, Michael R Johnson, Pauls Auce, Graeme J Sills, Larry W Baum, Pak C Sham, Stacey S Cherny, Colin H T Lui, Nina Barišić, Norman Delanty, Colin P Doherty, Arif Shukralla, Mark McCormack, Hany El-Naggar, Laura Canafoglia, Silvana Franceschetti, Barbara Castellotti, Tiziana Granata, Federico Zara, Michele Iacomino, Francesca Madia, Maria Stella Vari, Maria Margherita Mancardi, Vincenzo Salpietro, Francesca Bisulli, Paolo Tinuper, Laura Licchetta, Tommaso Pippucci, Carlotta Stipa, Raffaella Minardi, Antonio Gambardella, Angelo Labate, Grazia Annesi, Lorella Manna, Monica Gagliardi, Elena Parrini, Davide Mei, Annalisa Vetro, Claudia Bianchini, Martino Montomoli, Viola Doccini, Carla Marini, Toshimitsu Suzuki, Yushi Inoue, Kazuhiro Yamakawa, Birute Tumiene, Lynette G Sadleir, Chontelle King, Emily Mountier, Hande S Caglayan, Mutluay Arslan, Zuhal Yapıcı, Uluc Yis, Pınar Topaloglu, Bulent Kara, Dilsad Turkdogan, Aslı Gundogdu-Eken, Nerses Bebek, Sibel Uğur-İşeri, Betül Baykan, Barış Salman, Garen Haryanyan, Emrah Yücesan, Yeşim Kesim, Çiğdem Özkara, Annapurna Poduri, Beth R Shiedley, Catherine Shain, Russell J Buono, Thomas N Ferraro, Michael R Sperling, Warren Lo, Michael Privitera, Jacqueline A French, Steven Schachter, Ruben I Kuzniecky, Orrin Devinsky, Manu Hegde, Pouya Khankhanian, Katherine L Helbig, Colin A Ellis, Gianfranco Spalletta, Fabrizio Piras, Federica Piras, Tommaso Gili, Valentina Ciullo, Andreas Reif, Andrew McQuillin, Nick Bass, Andrew McIntosh, Douglas Blackwood, Mandy Johnstone, Aarno Palotie, Michele T Pato, Carlos N Pato, Evelyn J Bromet, Celia Barreto Carvalho, Eric D Achtyes, Maria Helena Azevedo, Roman Kotov, Douglas S Lehrer, Dolores Malaspina, Stephen R Marder, Helena Medeiros, Christopher P Morley, Diana O Perkins, Janet L Sobell, Peter F Buckley, Fabio Macciardi, Mark H Rapaport, James A Knowles, Genomic Psychiatry Cohort, Ayman H Fanous, Steven A McCarroll, Namrata Gupta, Stacey B Gabriel, Mark J Daly, Eric S Lander, Daniel H Lowenstein, David B Goldstein, Samuel F Berkovic, Benjamin M Neale, Epi25 Collaborative, Koko M., Krause R., Sander T., Bobbili D.R., Nothnagel M., May P., Lerche H., Bisulli F., Tinuper P., Pippucci T., Abbott, Liam E., Hengsbach, Christian, Rau, Sarah, Maisch, Ana F., Steinhoff, Bernhard J., Schulze-Bonhage, Andreas, Schubert-Bast, Susanne, Schreiber, Herbert, Borggräfe, Ingo, Schankin, Christoph J., Mayer, Thomas, Tashman, Katherine, Korinthenberg, Rudolf, Brockmann, Knut, Kurlemann, Gerhard, Dennig, Dieter, Madeleyn, Rene, Kälviäinen, Reetta, Auvinen, Pia, Saarela, Anni, Linnankivi, Tarja, Lehesjoki, Anna-Elina, Cerrato, Felecia, Rees, Mark I., Chung, Seo-Kyung, Pickrell, William O., Powell, Robert, Schneider, Natascha, Balestrini, Simona, Zagaglia, Sara, Braatz, Vera, Johnson, Michael R., Auce, Pauls, Singh, Tarjinder, Sills, Graeme J., Baum, Larry W., Sham, Pak C., Cherny, Stacey S., Lui, Colin H. T., Barišic, Nina, Delanty, Norman, Doherty, Colin P., Shukralla, Arif, McCormack, Mark, Heyne, Henrike, El-Naggar, Hany, Canafoglia, Laura, Franceschetti, Silvana, Castellotti, Barbara, Granata, Tiziana, Zara, Federico, Iacomino, Michele, Madia, Francesca, Vari, Maria Stella, Mancardi, Maria Margherita, Byrnes, Andrea, Salpietro, Vincenzo, Bisulli, Francesca, Tinuper, Paolo, Licchetta, Laura, Pippucci, Tommaso, Stipa, Carlotta, Minardi, Raffaella, Gambardella, Antonio, Labate, Angelo, Annesi, Grazia, Churchhouse, Claire, Manna, Lorella, Gagliardi, Monica, Parrini, Elena, Mei, Davide, Vetro, Annalisa, Bianchini, Claudia, Montomoli, Martino, Doccini, Viola, Marini, Carla, Suzuki, Toshimitsu, Watts, Nick, Inoue, Yushi, Yamakawa, Kazuhiro, Tumiene, Birute, Sadleir, Lynette G., King, Chontelle, Mountier, Emily, Caglayan, Hande S., Arslan, Mutluay, Yapici, Zuhal, Yis, Uluc, Solomonson, Matthew, Topaloglu, Pinar, Kara, Bulent, Turkdogan, Dilsad, Gundogdu-Eken, Asli, Bebek, Nerses, Ugur-Iseri, Sibel, Baykan, Betül, Salman, Baris, Haryanyan, Garen, Yücesan, Emrah, Lal, Dennis, Kesim, Yesim, Özkara, Çigdem, Poduri, Annapurna, Shiedley, Beth R., Shain, Catherine, Buono, Russell J., Ferraro, Thomas N., Sperling, Michael R., Lo, Warren, Privitera, Michael, Heinzen, Erin L., French, Jacqueline A., Schachter, Steven, Kuzniecky, Ruben I., Devinsky, Orrin, Hegde, Manu, Khankhanian, Pouya, Helbig, Katherine L., Ellis, Colin A., Spalletta, Gianfranco, Piras, Fabrizio, Dhindsa, Ryan S., Piras, Federica, Gili, Tommaso, Ciullo, Valentina, Reif, Andreas, McQuillin, Andrew, Bass, Nick, McIntosh, Andrew, Blackwood, Douglas, Johnstone, Mandy, Palotie, Aarno, Stanley, Kate E., Pato, Michele T., Pato, Carlos N., Bromet, Evelyn J., Carvalho, Celia Barreto, Achtyes, Eric D., Azevedo, Maria Helena, Kotov, Roman, Lehrer, Douglas S., Malaspina, Dolores, Marder, Stephen R., Cavalleri, Gianpiero L., Medeiros, Helena, Morley, Christopher P., Perkins, Diana O., Sobell, Janet L., Buckley, Peter F., Macciardi, Fabio, Rapaport, Mark H., Knowles, James A., Cohort, Genomic Psychiatry, Fanous, Ayman H., Hakonarson, Hakon, McCarroll, Steven A., Gupta, Namrata, Gabriel, Stacey B., Daly, Mark J., Lander, Eric S., Lowenstein, Daniel H., Goldstein, David B., Lerche, Holger, Berkovic, Samuel F., Neale, Benjamin M., Helbig, Ingo, Krause, Roland, May, Patrick, Weckhuysen, Sarah, Petrovski, Slavé, Kamalakaran, Sitharthan, Sisodiya, Sanjay M., Cossette, Patrick, Cotsapas, Chris, DeJonghe, Peter, Dixon-Salazar, Tracy, Guerrini, Renzo, Kwan, Patrick, Marson, Anthony G., Stewart, Randy, Depondt, Chantal, Dlugos, Dennis J., Scheffer, Ingrid E., Striano, Pasquale, Freyer, Catharine, McKenna, Kevin, Regan, Brigid M., Bellows, Susannah T., Leu, Costin, Bennett, Caitlin A., Johns, Esther M. C., Macdonald, Alexandra, Shilling, Hannah, Burgess, Rosemary, Weckhuysen, Dorien, Bahlo, Melanie, O'Brien, Terence J., Todaro, Marian, Stamberger, Hannah, Andrade, Danielle M., Sadoway, Tara R., Mo, Kelly, Krestel, Heinz, Gallati, Sabina, Papacostas, Savvas S., Kousiappa, Ioanna, Tanteles, George A., Šterbová, Katalin, Vlcková, Markéta, Sedlácková, Lucie, Laššuthová, Petra, Klein, Karl Martin, Rosenow, Felix, Reif, Philipp S., Knake, Susanne, Kunz, Wolfram S., Zsurka, Gábor, Elger, Christian E., Bauer, Jürgen, Rademacher, Michael, Feng, Yen-Chen Anne, Pendziwiat, Manuela, Muhle, Hiltrud, Rademacher, Annika, van Baalen, Andreas, von Spiczak, Sarah, Stephani, Ulrich, Afawi, Zaid, Korczyn, Amos D., Kanaan, Moien, Canavati, Christina, Howrigan, Daniel P., Müller-Schlüter, Karen, Kluger, Gerhard, Häusler, Martin, Blatt, Ilan, Lemke, Johannes R., Krey, Ilona, Weber, Yvonne G., Wolking, Stefan, Becker, Felicitas, DFG Research Unit FOR-2715 (Germany), FNR (Luxembourg), NHGRI (US), NHLBI (US), DAAD (Germany). [sponsor], and Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center]

Subjects
Exome sequencing, Male, Medicine (General), Neurology [D14] [Human health sciences], Gene-set, Genome-wide association study, Disease, Biology, Epileptogenesis, General Biochemistry, Genetics and Molecular Biology, Whole Exome Sequencing, Epilepsy, R5-920, medicine, Missense mutation, Humans, Exome, Genetic Predisposition to Disease, Gene, Genetic association, Ultra-rare variant, Genetics, Neurologie [D14] [Sciences de la santé humaine], Burden analysis, Genetic Variation, General Medicine, medicine.disease, Ultra-rare variants, Gene-sets, Case-Control Studies, Medicine, epilepsy, Epilepsy, Generalized, Female, Genetics & genetic processes [F10] [Life sciences], Epilepsies, Partial, Human medicine, Burden analysi, Génétique & processus génétiques [F10] [Sciences du vivant], Case-Control Studie, Research Paper, Genome-Wide Association Study, Human
Abstract

EBioMedicine 72, 103588 (2021). doi:10.1016/j.ebiom.2021.103588, Published by Elsevier, Amsterdam [u.a.]

Published
2021
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8. Sub-genic intolerance, ClinVar, and the epilepsies: A whole-exome sequencing study of 29,165 individuals

Author

Joshua E. Motelow, Gundula Povysil, Ryan S. Dhindsa, Kate E. Stanley, Andrew S. Al- len, Yen-Chen Anne Feng, Daniel P. Howrigan, Liam E. Abbott, Ka- therine Tashman, Felecia Cerrato, Caroline Cusick, Tarjinder Singh, Henrike Heyne, Andrea E. Byrnes, Claire Churchhouse, Nick Watts, Matthew Solomonson, Dennis Lal, Namrata Gupta, Benjamin M. Neale, Gianpiero L. Cavalleri, Patrick Cossette, Chris Cotsapas, Peter De Jonghe, Tracy Dixon-Salazar, Renzo Guerrini, Hakon Hakonarson, Erin L. Heinzen, Ingo Helbig, Patrick Kwan, Anthony G. Marson, Slave ? Petrovski, Sitharthan Kamalakaran, Sanjay M. Sisodiya, Randy Stewart, Sarah Weckhuysen, Chantal Depondt, Dennis J. Dlugos, Ingrid E. Scheffer, Pasquale Striano, Catharine Freyer, Roland Krause, Patrick May, Kevin McKenna, Brigid M. Regan, Caitlin A. Bennett, Costin Leu, Stephanie L. Leech, Terence J. O'Brien, Marian Todaro, Hannah Stamberger, Danielle M. Andrade, Quratulain Zulfiqar Ali, Tara R. Sadoway, Heinz Krestel, Andre ? Schaller, Savvas S. Papacostas, Ioanna Kou- siappa, George A. Tanteles, Yiolanda Christou, Katalin Sterbova ?, Marke ? ta Vlckova ?, Lucie Sedlackova, Petra Lassuthova ?, Karl Martin Klein, Felix Rosenow, Philipp S. Reif, Susanne Knake, Bernd A. Neubauer, Friedrich Zimprich, Martha Feucht, Eva M. Reinthaler, Wolfram S. Kunz, Ga ?bor Zsurka, Rainer Surges, Tobias Baumgart- ner, Randi von Wrede, Manuela Pendziwiat, Hiltrud Muhle, An- nika Rademacher, Andreas van Baalen, Sarah von Spiczak, Ulrich Stephani, Zaid Afawi, Amos D. Korczyn, Moien Kanaan, Christina Canavati, Gerhard Kurlemann, Karen Mu ?ller-Schlu ?ter, Gerhard Kluger, Martin Ha ?usler, Ilan Blatt, Johannes R. Lemke, Ilona Krey, Yvonne G. Weber, Stefan Wolking, Felicitas Becker, Stephan Lauxmann, Christian Boßelmann, Josua Kegele, Christian Hengs- bach, Sarah Rau, Bernhard J. Steinhoff, Andreas Schulze-Bonhage, IngoBorggra ?fe, ChristophJ.Schankin, SusanneSchubert-Bast, Herbert Schreiber, Thomas Mayer, Rudolf Korinthenberg, Knut Brockmann, Markus Wolff, Dieter Dennig, Rene Madeleyn, Reetta Ka ?lvia ?inen, Anni Saarela, Oskari Timonen, Tarja Linnankivi, Anna-Elina Lehesjoki, Sylvain Rheims, Gaetan Lesca, Philippe Ryvlin, Louis Maillard, Luc Valton, Philippe Derambure, Fabrice Bartolomei, Edouard Hirsch, Ve ?ronique Michel, Francine Chas- soux, Mark I. Rees, Seo-Kyung Chung, William O. Pickrell, Robert Powell, Mark D. Baker, Beata Fonferko-Shadrach, Charlotte Law- thom, Joseph Anderson, Natascha Schneider, Simona Balestrini, Sara Zagaglia, Vera Braatz, Michael R. Johnson, Pauls Auce, Graeme J. Sills, Larry W. Baum, Pak C. Sham, Stacey S. Cherny, Colin H.T. Lui, Norman Delanty, Colin P. Doherty, Arif Shukralla, Hany El-Naggar, Peter Widdess-Walsh, Nina Barisic, Laura 12 The American Journal of Human Genetics 108, 1-18, June 3, 2021 Please cite this article in press as: Epi25 Collaborative, Sub-genic intolerance, ClinVar, the epilepsies: A whole-exome sequencing study of 29, 165 individuals, The American Journal of Human Genetics (2021), https://doi.org/10.1016/j.ajhg.2021.04.009 Canafoglia, Silvana Franceschetti, Barbara Castellotti, Tiziana Granata, Francesca Ragona, Federico Zara, Michele Iacomino, An- tonella Riva, Francesca Madia, Maria Stella Vari, Vincenzo Salpie- tro, Marcello Scala, Maria Margherita Mancardi, Lino Nobili, Elisa- betta Amadori, Thea Giacomini, Francesca Bisulli, Tommaso Pippucci, Laura Licchetta, Raffaella Minardi, Paolo Tinuper, Lor- enzo Muccioli, Barbara Mostacci, Antonio Gambardella, Angelo Labate, Grazia Annesi, Lorella Manna, Monica Gagliardi, Elena Parrini, Davide Mei, Annalisa Vetro, Claudia Bianchini, Martino Montomoli, Viola Doccini, Carmen Barba, Shinichi Hirose, At- sushi Ishii, Toshimitsu Suzuki, Yushi Inoue, Kazuhiro Yamakawa, Ahmad Beydoun, Wassim Nasreddine, Nathalie Khoueiry Zgheib, Birute Tumiene, Algirdas Utkus, Lynette G. Sadleir, Chontelle King, S. Hande Caglayan, Mutluay Arslan, Zuhal Yap?c?, P?nar To- paloglu, Bulent Kara, Uluc Yis, Dilsad Turkdogan, Asl? Gun- dogdu-Eken, Nerses Bebek, Meng-Han Tsai, Chen-Jui Ho, Chih- Hsiang Lin, Kuang-Lin Lin, I-Jun Chou, Annapurna Poduri, Beth R. Shiedley, Catherine Shain, Jeffrey L. Noebels, Alicia Goldman, Robyn M. Busch, Lara Jehi, Imad M. Najm, Lisa Ferguson, Jean Khoury, Tracy A. Glauser, Peggy O. Clark, Russell J. Buono, Thomas N. Ferraro, Michael R. Sperling, Warren Lo, Michael Privitera, Jac- queline A. French, Steven Schachter, Ruben I. Kuzniecky, Orrin Devinsky, Manu Hegde, David A. Greenberg, Colin A. Ellis, Ethan Goldberg, Katherine L. Helbig, Mahgenn Cosico, Priya Vaidis- waran, Eryn Fitch, Samuel F. Berkovic, Holger Lerche, Daniel H. Lowenstein, David B. Goldstein., Motelow J.E., Povysil G., Dhindsa R.S., Stanley K.E., Allen A.S., Feng Y.-C.A., Howrigan D.P., Abbott L.E., Tashman K., Cerrato F., Cusick C., Singh T., Heyne H., Byrnes A.E., Churchhouse C., Watts N., Solomonson M., Lal D., Gupta N., Neale B.M., Cavalleri G.L., Cossette P., Cotsapas C., De Jonghe P., Dixon-Salazar T., Guerrini R., Hakonarson H., Heinzen E.L., Helbig I., Kwan P., Marson A.G., Petrovski S., Kamalakaran S., Sisodiya S.M., Stewart R., Weckhuysen S., Depondt C., Dlugos D.J., Scheffer I.E., Striano P., Freyer C., Krause R., May P., McKenna K., Regan B.M., Bennett C.A., Leu C., Leech S.L., O'Brien T.J., Todaro M., Stamberger H., Andrade D.M., Ali Q.Z., Sadoway T.R., Krestel H., Schaller A., Papacostas S.S., Kousiappa I., Tanteles G.A., Christou Y., Sterbova K., Vlckova M., Sedlackova L., Lassuthova P., Klein K.M., Rosenow F., Reif P.S., Knake S., Neubauer B.A., Zimprich F., Feucht M., Reinthaler E.M., Kunz W.S., Zsurka G., Surges R., Baumgartner T., von Wrede R., Pendziwiat M., Muhle H., Rademacher A., van Baalen A., von Spiczak S., Stephani U., Afawi Z., Korczyn A.D., Kanaan M., Canavati C., Kurlemann G., Muller-Schluter K., Kluger G., Hausler M., Blatt I., Lemke J.R., Krey I., Weber Y.G., Wolking S., Becker F., Lauxmann S., Bosselmann C., Kegele J., Hengsbach C., Rau S., Steinhoff B.J., Schulze-Bonhage A., Borggrafe I., Schankin C.J., Schubert-Bast S., Schreiber H., Mayer T., Korinthenberg R., Brockmann K., Wolff M., Dennig D., Madeleyn R., Kalviainen R., Saarela A., Timonen O., Linnankivi T., Lehesjoki A.-E., Rheims S., Lesca G., Ryvlin P., Maillard L., Valton L., Derambure P., Bartolomei F., Hirsch E., Michel V., Chassoux F., Rees M.I., Chung S.-K., Pickrell W.O., Powell R., Baker M.D., Fonferko-Shadrach B., Lawthom C., Anderson J., Schneider N., Balestrini S., Zagaglia S., Braatz V., Johnson M.R., Auce P., Sills G.J., Baum L.W., Sham P.C., Cherny S.S., Lui C.H.T., Delanty N., Doherty C.P., Shukralla A., El-Naggar H., Widdess-Walsh P., Barisic N., Canafoglia L., Franceschetti S., Castellotti B., Granata T., Ragona F., Zara F., Iacomino M., Riva A., Madia F., Vari M.S., Salpietro V., Scala M., Mancardi M.M., Nobili L., Amadori E., Giacomini T., Bisulli F., Pippucci T., Licchetta L., Minardi R., Tinuper P., Muccioli L., Mostacci B., Gambardella A., Labate A., Annesi G., Manna L., Gagliardi M., Parrini E., Mei D., Vetro A., Bianchini C., Montomoli M., Doccini V., Barba C., Hirose S., Ishii A., Suzuki T., Inoue Y., Yamakawa K., Beydoun A., Nasreddine W., Khoueiry Zgheib N., Tumiene B., Utkus A., Sadleir L.G., King C., Caglayan S.H., Arslan M., Yapici Z., Topaloglu P., Kara B., Yis U., Turkdogan D., Gundogdu-Eken A., Bebek N., Tsai M.-H., Ho C.-J., Lin C.-H., Lin K.-L., Chou I.-J., Poduri A., Shiedley B.R., Shain C., Noebels J.L., Goldman A., Busch R.M., Jehi L., Najm I.M., Ferguson L., Khoury J., Glauser T.A., Clark P.O., Buono R.J., Ferraro T.N., Sperling M.R., Lo W., Privitera M., French J.A., Schachter S., Kuzniecky R.I., Devinsky O., Hegde M., Greenberg D.A., Ellis C.A., Goldberg E., Helbig K.L., Cosico M., Vaidiswaran P., Fitch E., Berkovic S.F., Lerche H., Lowenstein D.H., Goldstein D.B., Epi25 Collaborative, Institut de Neurosciences des Systèmes (INS), and Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
0301 basic medicine, focal epilepsy, Whole Exome Sequencing, Cohort Studies, Epilepsy, 0302 clinical medicine, Genetic Marker, Missense mutation, Exome, whole-exome sequencing, generalized epilepsy, ComputingMilieux_MISCELLANEOUS, Genetics (clinical), Exome sequencing, seizures, Genetics, ClinVar, Phenotype, epileptic encephalopathy, Epi25, intolerance, Case-Control Studie, Human, Genetic Markers, seizure, Disease Association, Biology, Article, 03 medical and health sciences, Exome Sequencing, medicine, Humans, Genetic Predisposition to Disease, Genetic Testing, Generalized epilepsy, Gene, Louvain, [SCCO.NEUR]Cognitive science/Neuroscience, Correction, Genetic Variation, medicine.disease, epilepsy, Human genetics, 030104 developmental biology, Case-Control Studies, Human medicine, Cohort Studie, Genetic generalized epilepsy, 030217 neurology & neurosurgery
Abstract

Summary Both mild and severe epilepsies are influenced by variants in the same genes, yet an explanation for the resulting phenotypic variation is unknown. As part of the ongoing Epi25 Collaboration, we performed a whole-exome sequencing analysis of 13,487 epilepsy-affected individuals and 15,678 control individuals. While prior Epi25 studies focused on gene-based collapsing analyses, we asked how the pattern of variation within genes differs by epilepsy type. Specifically, we compared the genetic architectures of severe developmental and epileptic encephalopathies (DEEs) and two generally less severe epilepsies, genetic generalized epilepsy and non-acquired focal epilepsy (NAFE). Our gene-based rare variant collapsing analysis used geographic ancestry-based clustering that included broader ancestries than previously possible and revealed novel associations. Using the missense intolerance ratio (MTR), we found that variants in DEE-affected individuals are in significantly more intolerant genic sub-regions than those in NAFE-affected individuals. Only previously reported pathogenic variants absent in available genomic datasets showed a significant burden in epilepsy-affected individuals compared with control individuals, and the ultra-rare pathogenic variants associated with DEE were located in more intolerant genic sub-regions than variants associated with non-DEE epilepsies. MTR filtering improved the yield of ultra-rare pathogenic variants in affected individuals compared with control individuals. Finally, analysis of variants in genes without a disease association revealed a significant burden of loss-of-function variants in the genes most intolerant to such variation, indicating additional epilepsy-risk genes yet to be discovered. Taken together, our study suggests that genic and sub-genic intolerance are critical characteristics for interpreting the effects of variation in genes that influence epilepsy.

Published
2021
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9. De Novo Mutations in PPP3CA Cause Severe Neurodevelopmental Disease with Seizures

Author

Annapurna Poduri, Samuel F. Berkovic, Candace T. Myers, Deepali N. Shinde, Arezoo Rezazadeh, Karen Oliver, Ingrid E. Scheffer, Heather C Mefford, Emily I. Mountier, Lynette G. Sadleir, Michal Tzadok, Saskia Freytag, Maureen S. Mulhern, Zhong Ren, Erin L. Heinzen, Melanie Bahlo, Michelle E. Ernst, Natalie Lippa, Danielle M. Andrade, Brigid M. Regan, Nicholas Stong, Katherine L. Helbig, Bruria Ben Zeev, Gali Heimer, Lynne M. Bird, Daniel H. Lowenstein, Joseph Sullivan, David Goldstein, and Andreea Nissenkorn

Subjects
Male, 0301 basic medicine, Neurodegenerative, medicine.disease_cause, Bioinformatics, Infantile, Severity of Illness Index, Synaptic Transmission, Medical and Health Sciences, Spasms, Cohort Studies, Epilepsy, 2.1 Biological and endogenous factors, STXBP1, Exome, Aetiology, Child, calcineurin, Genetics (clinical), Exome sequencing, Pediatric, Genetics & Heredity, Genetics, Mutation, Calcineurin, Biological Sciences, PPP3CA, Child, Preschool, Neurological, Female, Spasms, Infantile, Sequence Analysis, Adult, Adolescent, Biology, Article, Young Adult, 03 medical and health sciences, medicine, Humans, Synaptic vesicle recycling, developmental and epileptic encephalopathy, Preschool, Lennox Gastaut Syndrome, Genetic heterogeneity, Infant, Newborn, Neurosciences, Infant, Sequence Analysis, DNA, DNA, Newborn, medicine.disease, de novo mutation, Brain Disorders, Good Health and Well Being, 030104 developmental biology, Neurodevelopmental Disorders, Lennox–Gastaut syndrome
Abstract

Exome sequencing has readily enabled the discovery of the genetic mutations responsible for a wide range of diseases. This success has been particularly remarkable in the severe epilepsies and other neurodevelopmental diseases for which rare, often de novo , mutations play a significant role in disease risk. Despite significant progress, the high genetic heterogeneity of these disorders often requires large sample sizes to identify a critical mass of individuals with disease-causing mutations in a single gene. By pooling genetic findings across multiple studies, we have identified six individuals with severe developmental delay (6/6), refractory seizures (5/6), and similar dysmorphic features (3/6), each harboring a de novo mutation in PPP3CA . PPP3CA encodes the alpha isoform of a subunit of calcineurin. Calcineurin encodes a calcium- and calmodulin-dependent serine/threonine protein phosphatase that plays a role in a wide range of biological processes, including being a key regulator of synaptic vesicle recycling at nerve terminals. Five individuals with de novo PPP3CA mutations were identified among 4,760 trio probands with neurodevelopmental diseases; this is highly unlikely to occur by chance (p = 1.2 × 10 −8 ) given the size and mutability of the gene. Additionally, a sixth individual with a de novo mutation in PPP3CA was connected to this study through GeneMatcher. Based on these findings, we securely implicate PPP3CA in early-onset refractory epilepsy and further support the emerging role for synaptic dysregulation in epilepsy.

Published
2017
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10. Disruptive mutations in TANC2 define a neurodevelopmental syndrome associated with psychiatric disorders

Author

Charles E. Schwartz, Marjolein H. Willemsen, Saadet Mercimek-Andrews, Amy B. Wilfert, Hugo J. Bellen, Alexander P.A. Stegmann, Tjitske Kleefstra, Pawel Stankiewicz, Benjamin Büttner, Hailun Ni, Rongjuan Zhao, Rami Abou Jamra, Mariëtte J.V. Hoffer, Kristin Herman, Marjan M. Weiss, Heather C Mefford, Huidan Wu, Deanna J. Erwin, Zhengmao Hu, Claudia A. L. Ruivenkamp, Helger G. Yntema, Cindy Colson, Alessandra Murgia, Maria Bottitta, Jane Juusola, Tianyun Wang, Stephen M. Malone, Kun Xia, Baosheng Zhu, Nicolas Richard, Jozef Gecz, Elisa Bettella, Tuula Rinne, Raphael Bernier, Emilia K. Bijlsma, Michael F. Wangler, Shinya Yamamoto, Brigid M. Regan, Sharayu Jangam, Bregje W.M. van Bon, Jill A. Rosenfeld, Kendra Hoekzema, Cenying Liu, Shweta U. Dhar, Stefano Sartori, Boris Keren, Hui Guo, Lucia Castiglia, Servi J. C. Stevens, Corrado Romano, Min Long, Tomasz J. Nowakowski, Evan E. Eichler, Jan Maarten Cobben, Alison M. Muir, Lisa Emrick, Quinten Waisfisz, Wenjing Zhao, Jonathan C. Andrews, Ingrid E. Scheffer, Bing Bai, Madelyn A. Gillentine, Paul C. Marcogliese, Fan Xia, Han G. Brunner, Alexandra Afenjar, Academic Medical Center, MUMC+: DA KG Polikliniek (9), MUMC+: DA KG Lab Centraal Lab (9), RS: GROW - R4 - Reproductive and Perinatal Medicine, MUMC+: DA Klinische Genetica (5), Klinische Genetica, Chinese Academy of Forestry, University Hospital of Padua, Baylor College of Medicine (BCM), Baylor University, Texas Children's Hospital [Houston, USA], Central South University [Changsha], University of California, Washington University School of Medicine in St. Louis, Washington University in Saint Louis (WUSTL), Department of Genome Sciences [Seattle] (GS), University of Washington [Seattle], Radboud University Medical Center [Nijmegen], Maastricht University Medical Centre (MUMC), Maastricht University [Maastricht], Ecosystèmes méditerranéens et risques (UR EMAX), Centre national du machinisme agricole, du génie rural, des eaux et forêts (CEMAGREF), Service de Génétique [CHU Caen], Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-CHU Caen, Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN)-Tumorothèque de Caen Basse-Normandie (TCBN), Biologie, génétique et thérapies ostéoarticulaires et respiratoires (BIOTARGEN), Normandie Université (NU)-Normandie Université (NU), The Greenwood Genetic Center, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Fondazione 'Istituto Neurologico Nazionale C. Mondino', Centre de Recherche de l'Institut du Cerveau et de la Moelle épinière (CRICM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), CHU Trousseau [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Kunming University of Science and Technology (KMUST), The Hospital for sick children [Toronto] (SickKids), University of Toronto, GeneDx [Gaithersburg, MD, USA], Universität Leipzig [Leipzig], University of Melbourne, Queensland Institute of Medical Research, University of Adelaide, Emma Children’s Hospital, Vrije Universiteit Amsterdam [Amsterdam] (VU), Leiden University Medical Center (LUMC), The Chinese University of Hong Kong [Hong Kong], and Human genetics

Subjects
0301 basic medicine, Proband, Male, Genetics of the nervous system, Developmental Disabilities, General Physics and Astronomy, Muscle Proteins, medicine.disease_cause, ANNOTATION, Sensory disorders Donders Center for Medical Neuroscience [Radboudumc 12], Whole Exome Sequencing, Craniofacial Abnormalities, Epilepsy, 0302 clinical medicine, Postsynaptic potential, Intellectual disability, Drosophila Proteins, lcsh:Science, Child, SYNAPTIC DEVELOPMENT, Neurons, Mutation, Multidisciplinary, Behavior, Animal, Mental Disorders, Brain, Drosophila melanogaster, Child, Preschool, Behavioural genetics, Excitatory postsynaptic potential, Female, Neuroglia, Rare cancers Radboud Institute for Health Sciences [Radboudumc 9], Adult, medicine.medical_specialty, GENES, Adolescent, Science, Nerve Tissue Proteins, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Young Adult, All institutes and research themes of the Radboud University Medical Center, RESOURCE, Intellectual Disability, Exome Sequencing, medicine, Animals, Humans, Language Development Disorders, Autistic Disorder, Psychiatry, Preschool, [SDV.GEN]Life Sciences [q-bio]/Genetics, Behavior, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], business.industry, Animal, MEMORY, Membrane Proteins, Proteins, General Chemistry, medicine.disease, FRAMEWORK, 030104 developmental biology, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, DE-NOVO MUTATIONS, Neurodevelopmental Disorders, Neuronal development, Autism, lcsh:Q, business, Postsynaptic density, 030217 neurology & neurosurgery
Abstract

Postsynaptic density (PSD) proteins have been implicated in the pathophysiology of neurodevelopmental and psychiatric disorders. Here, we present detailed clinical and genetic data for 20 patients with likely gene-disrupting mutations in TANC2—whose protein product interacts with multiple PSD proteins. Pediatric patients with disruptive mutations present with autism, intellectual disability, and delayed language and motor development. In addition to a variable degree of epilepsy and facial dysmorphism, we observe a pattern of more complex psychiatric dysfunction or behavioral problems in adult probands or carrier parents. Although this observation requires replication to establish statistical significance, it also suggests that mutations in this gene are associated with a variety of neuropsychiatric disorders consistent with its postsynaptic function. We find that TANC2 is expressed broadly in the human developing brain, especially in excitatory neurons and glial cells, but shows a more restricted pattern in Drosophila glial cells where its disruption affects behavioral outcomes., Neurodevelopmental disorders (NDDs) are a heterogeneous group of diseases for which the genetic basis is still unknown in more than half of the cases. Here, the authors report a NDD associated with disruptive variants in the TANC2 gene and show that rols, the TANC2 homolog in flies, is required for synapse growth and function.

Published
2019
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11. SLC35A2-CDG: Functional Characterization, Expanded Molecular, Clinical, and Biochemical Phenotypes of 30 Unreported Individuals

Author

Jesse M. Hunter, Mary S. Willis, Bryce A. Mendelsohn, Sha Tang, Carlos A. Bacino, Eric Vilain, Hane Lee, Jill A. Rosenfeld, Delphine Héron, Tyler Mark Pierson, Zöe Powis, Shenela Lakhani, Naghmeh Dorrani, Lorenzo D. Botto, Maria J. Guillen Sacoto, Jaclyn Haven, Julie S. Cohen, Trine Bjørg Hammer, Bobby G. Ng, Charles Marques Lourenço, Rita Barone, Jennifer Burton, Ingrid E. Scheffer, Wendy G. Mitchell, Pasquale Striano, Stephanie Grunewald, Stanley F. Nelson, Nicola Longo, Jane Juusola, Fernando Scaglia, Christopher C.Y. Mak, Hudson H. Freeze, Shoji Yano, Leon G. Epstein, Arthur Partikian, Domenico Garozzo, Mohammed Almannai, Joy Lee, Hui Yang, Dianalee McKnight, Abdallah F. Elias, William A. Gahl, Nilika S. Singhal, Christina G.S. Palmer, Devorah Segal, Andrew C. Edmondson, George E. Hoganson, Cyril Mignot, Brian H.Y. Chung, Colleen M. Carlston, Mahim Jain, M. Elizabeth Ross, Paulina Sosicka, David Coman, Sharon F. Suchy, Shane C. Quinonez, Ghayda M. Mirzaa, Katrina M. Dipple, Satish Agadi, Joseph D. Symonds, Lynne A. Wolfe, Marc C. Patterson, Brigid M. Regan, Luisa Sturiale, Mariusz Olczak, Hiltrud Muhle, Katherine Lewis, William B. Dobyns, and Matthew R. Herzog

Subjects
UDP-galactose, congenital disorders of glycosylation, glycoside, nucleotide sugar transporter, Male, Glycosylation, Monosaccharide Transport Proteins, Cells, Biopsy, Clinical Sciences, CHO Cells, Biology, medicine.disease_cause, Article, Uridine Diphosphate Galactose, 03 medical and health sciences, chemistry.chemical_compound, Congenital Disorders of Glycosylation, Cricetulus, Clinical Research, Genetics, medicine, 2.1 Biological and endogenous factors, Animals, Humans, Aetiology, Allele, Gene, Genetics (clinical), Cells, Cultured, 030304 developmental biology, Pediatric, Genetics & Heredity, 0303 health sciences, Mutation, Cultured, 030305 genetics & heredity, medicine.disease, Phenotype, Biomarker (cell), carbohydrates (lipids), chemistry, Female, Lipid glycosylation, Congenital disorder of glycosylation
Abstract

Pathogenic de novo variants in the X-linked gene SLC35A2 encoding the major Golgi-localized UDP-galactose transporter required for proper protein and lipid glycosylation cause a rare type of congenital disorder of glycosylation known as SLC35A2-congenital disorders of glycosylation (CDG; formerly CDG-IIm). To date, 29 unique de novo variants from 32 unrelated individuals have been described in the literature. The majority of affected individuals are primarily characterized by varying degrees of neurological impairments with or without skeletal abnormalities. Surprisingly, most affected individuals do not show abnormalities in serum transferrin N-glycosylation, a common biomarker for most types of CDG. Here we present data characterizing 30 individuals and add 26 new variants, the single largest study involving SLC35A2-CDG. The great majority of these individuals had normal transferrin glycosylation. In addition, expanding the molecular and clinical spectrum of this rare disorder, we developed a robust and reliable biochemical assay to assess SLC35A2-dependent UDP-galactose transport activity in primary fibroblasts. Finally, we show that transport activity is directly correlated to the ratio of wild-type to mutant alleles in fibroblasts from affected individuals.

Published
2019
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12. Intronic ATTTC repeat expansions in STARD7 in familial adult myoclonic epilepsy linked to chromosome 2

Author

Marina A. J. Tijssen, Mark A. Corbett, Zaid Afawi, Paolo Tinuper, Shoji Tsuji, Rachel Straussberg, Ilan Blatt, Samuel F. Berkovic, Francesco Brancati, Amy L Schneider, Lynette G. Sadleir, Sanjay M. Sisodiya, Renzo Guerrini, Shreyasee Chakraborty, Alfredo Berardelli, Silvana Franceschetti, Jozef Gecz, Luciano Xumerle, Pierre Labauge, Liana Veneziano, Simona Balestrini, Ingo Helbig, Martin A. Smith, Laura Canafoglia, Carlo Di Bonaventura, Hiroyuki Ishiura, Boris Keren, Manuela Pendziwiat, Rahel T. Florian, Sylvie Forlani, Anne Fleur van Rootselaar, Giorgio Casari, Christel Depienne, Tommaso Pippucci, Douglas E. Crompton, Edouard Hirsch, Davide Mei, Laura Licchetta, Renee Carroll, Riaan van Coller, Ingrid E. Scheffer, Thessa Kroes, Pasquale Striano, Brigid M. Regan, Francesca Bisulli, Shaun Carswell, Antonio Suppa, Julien Buratti, Karl Martin Klein, Alison Gardner, Caroline Nava, Federico Zara, Melanie Bahlo, Sabine Kaya, Kathryn Friend, Antonietta Coppola, Massimo Delledonne, Aaron M. Wenger, Anthony Correll, Sara Baldassari, Arn M. J. M. van den Maagdenberg, Eric LeGuern, Rachael Catford, Gabrielle Rudolf, Salvatore Striano, Mark F. Bennett, Josemir W. Sander, Kirston Barton, Michele Iacomino, Corbett M.A., Kroes T., Veneziano L., Bennett M.F., Florian R., Schneider A.L., Coppola A., Licchetta L., Franceschetti S., Suppa A., Wenger A., Mei D., Pendziwiat M., Kaya S., Delledonne M., Straussberg R., Xumerle L., Regan B., Crompton D., van Rootselaar A.-F., Correll A., Catford R., Bisulli F., Chakraborty S., Baldassari S., Tinuper P., Barton K., Carswell S., Smith M., Berardelli A., Carroll R., Gardner A., Friend K.L., Blatt I., Iacomino M., Di Bonaventura C., Striano S., Buratti J., Keren B., Nava C., Forlani S., Rudolf G., Hirsch E., Leguern E., Labauge P., Balestrini S., Sander J.W., Afawi Z., Helbig I., Ishiura H., Tsuji S., Sisodiya S.M., Casari G., Sadleir L.G., van Coller R., Tijssen M.A.J., Klein K.M., van den Maagdenberg A.M.J.M., Zara F., Guerrini R., Berkovic S.F., Pippucci T., Canafoglia L., Bahlo M., Striano P., Scheffer I.E., Brancati F., Depienne C., Gecz J., Neurology, ANS - Brain Imaging, Movement Disorder (MD), Corbett, M. A., Kroes, T., Veneziano, L., Bennett, M. F., Florian, R., Schneider, A. L., Coppola, A., Licchetta, L., Franceschetti, S., Suppa, A., Wenger, A., Mei, D., Pendziwiat, M., Kaya, S., Delledonne, M., Straussberg, R., Xumerle, L., Regan, B., Crompton, D., van Rootselaar, A. -F., Correll, A., Catford, R., Bisulli, F., Chakraborty, S., Baldassari, S., Tinuper, P., Barton, K., Carswell, S., Smith, M., Berardelli, A., Carroll, R., Gardner, A., Friend, K. L., Blatt, I., Iacomino, M., Di Bonaventura, C., Striano, S., Buratti, J., Keren, B., Nava, C., Forlani, S., Rudolf, G., Hirsch, E., Leguern, E., Labauge, P., Balestrini, S., Sander, J. W., Afawi, Z., Helbig, I., Ishiura, H., Tsuji, S., Sisodiya, S. M., Casari, G., Sadleir, L. G., van Coller, R., Tijssen, M. A. J., Klein, K. M., van den Maagdenberg, A. M. J. M., Zara, F., Guerrini, R., Berkovic, S. F., Pippucci, T., Canafoglia, L., Bahlo, M., Striano, P., Scheffer, I. E., Brancati, F., Depienne, C., and Gecz, J.

Subjects
0301 basic medicine, Male, Myoclonus, Medizin, General Physics and Astronomy, Epilepsies, Myoclonic, Epilepsies, Intronic variant, repeat expansions,STARD7, familial adult myoclonic epilepsy, chromosome 2, Epilepsy, 0302 clinical medicine, DOMINANT CORTICAL TREMOR, EXPRESSION ANALYSIS, PEDIGREE, LOCUS, LINKAGE, GENE, 2P11.1-Q12.2, REFINEMENT, MUTATION, BAFME, lcsh:Science, Child, Genetics, Multidisciplinary, DNA Repeat Expansion, Disease genetics, Chromosome Mapping, Middle Aged, Pedigree, Myoclonic Epilepsy, Child, Preschool, Chromosomes, Human, Pair 2, Pair 2, STARD7, Female, Adolescent, Adult, Carrier Proteins, Humans, Young Adult, Introns, Human, Science, Locus (genetics), Biology, Chromosomes, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, medicine, Preschool, Gene, Whole genome sequencing, Intron, Chromosome, General Chemistry, medicine.disease, 030104 developmental biology, Microsatellite instability, Myoclonic epilepsy, lcsh:Q, Familial Adult Myoclonic Epilepsy, Myoclonic, Carrier Protein, 030217 neurology & neurosurgery, Neurological disorders
Abstract

Familial Adult Myoclonic Epilepsy (FAME) is characterised by cortical myoclonic tremor usually from the second decade of life and overt myoclonic or generalised tonic-clonic seizures. Four independent loci have been implicated in FAME on chromosomes (chr) 2, 3, 5 and 8. Using whole genome sequencing and repeat primed PCR, we provide evidence that chr2-linked FAME (FAME2) is caused by an expansion of an ATTTC pentamer within the first intron of STARD7. The ATTTC expansions segregate in 158/158 individuals typically affected by FAME from 22 pedigrees including 16 previously reported families recruited worldwide. RNA sequencing from patient derived fibroblasts shows no accumulation of the AUUUU or AUUUC repeat sequences and STARD7 gene expression is not affected. These data, in combination with other genes bearing similar mutations that have been implicated in FAME, suggest ATTTC expansions may cause this disorder, irrespective of the genomic locus involved., Familial cortical myoclonic tremor (FAME) has so far been mapped to regions on chromosome 2, 3, 5 and 8 and pentameric repeat expansions in SAMD12 were identified as cause of FAME1. Here, Corbett et al. identify ATTTT/ATTTC repeat expansions in intron 1 of STARD7 in individuals with FAME2.”

Published
2019
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13. Ultra-Rare Genetic Variation in the Epilepsies: A Whole-Exome Sequencing Study of 17,606 Individuals

Author

Yen-Chen Anne Feng, Daniel P. Howrigan, Liam E. Abbott, Katherine Tashman, Felecia Cerrato, Tarjinder Singh, Henrike Heyne, Andrea Byrnes, Claire Churchhouse, Nick Watts, Matthew Solomonson, Dennis Lal, Erin L. Heinzen, Ryan S. Dhindsa, Kate E. Stanley, Gianpiero L. Cavalleri, Hakon Hakonarson, Ingo Helbig, Roland Krause, Patrick May, Sarah Weckhuysen, Slavé Petrovski, Sitharthan Kamalakaran, Sanjay M. Sisodiya, Patrick Cossette, Chris Cotsapas, Peter De Jonghe, Tracy Dixon-Salazar, Renzo Guerrini, Patrick Kwan, Anthony G. Marson, Randy Stewart, Chantal Depondt, Dennis J. Dlugos, Ingrid E. Scheffer, Pasquale Striano, Catharine Freyer, Kevin McKenna, Brigid M. Regan, Susannah T. Bellows, Costin Leu, Caitlin A. Bennett, Esther M.C. Johns, Alexandra Macdonald, Hannah Shilling, Rosemary Burgess, Dorien Weckhuysen, Melanie Bahlo, Terence J. O’Brien, Marian Todaro, Hannah Stamberger, Danielle M. Andrade, Tara R. Sadoway, Kelly Mo, Heinz Krestel, Sabina Gallati, Savvas S. Papacostas, Ioanna Kousiappa, George A. Tanteles, Katalin Štěrbová, Markéta Vlčková, Lucie Sedláčková, Petra Laššuthová, Karl Martin Klein, Felix Rosenow, Philipp S. Reif, Susanne Knake, Wolfram S. Kunz, Gábor Zsurka, Christian E. Elger, Jürgen Bauer, Michael Rademacher, Manuela Pendziwiat, Hiltrud Muhle, Annika Rademacher, Andreas van Baalen, Sarah von Spiczak, Ulrich Stephani, Zaid Afawi, Amos D. Korczyn, Moien Kanaan, Christina Canavati, Gerhard Kurlemann, Karen Müller-Schlüter, Gerhard Kluger, Martin Häusler, Ilan Blatt, Johannes R. Lemke, Ilona Krey, Yvonne G. Weber, Stefan Wolking, Felicitas Becker, Christian Hengsbach, Sarah Rau, Ana F. Maisch, Bernhard J. Steinhoff, Andreas Schulze-Bonhage, Susanne Schubert-Bast, Herbert Schreiber, Ingo Borggräfe, Christoph J. Schankin, Thomas Mayer, Rudolf Korinthenberg, Knut Brockmann, Dieter Dennig, Rene Madeleyn, Reetta Kälviäinen, Pia Auvinen, Anni Saarela, Tarja Linnankivi, Anna-Elina Lehesjoki, Mark I. Rees, Seo-Kyung Chung, William O. Pickrell, Robert Powell, Natascha Schneider, Simona Balestrini, Sara Zagaglia, Vera Braatz, Michael R. Johnson, Pauls Auce, Graeme J. Sills, Larry W. Baum, Pak C. Sham, Stacey S. Cherny, Colin H.T. Lui, Nina Barišić, Norman Delanty, Colin P. Doherty, Arif Shukralla, Mark McCormack, Hany El-Naggar, Laura Canafoglia, Silvana Franceschetti, Barbara Castellotti, Tiziana Granata, Federico Zara, Michele Iacomino, Francesca Madia, Maria Stella Vari, Maria Margherita Mancardi, Vincenzo Salpietro, Francesca Bisulli, Paolo Tinuper, Laura Licchetta, Tommaso Pippucci, Carlotta Stipa, Raffaella Minardi, Antonio Gambardella, Angelo Labate, Grazia Annesi, Lorella Manna, Monica Gagliardi, Elena Parrini, Davide Mei, Annalisa Vetro, Claudia Bianchini, Martino Montomoli, Viola Doccini, Carla Marini, Toshimitsu Suzuki, Yushi Inoue, Kazuhiro Yamakawa, Birute Tumiene, Lynette G. Sadleir, Chontelle King, Emily Mountier, S. Hande Caglayan, Mutluay Arslan, Zuhal Yapıcı, Uluc Yis, Pınar Topaloglu, Bulent Kara, Dilsad Turkdogan, Aslı Gundogdu-Eken, Nerses Bebek, Sibel Uğur-İşeri, Betül Baykan, Barış Salman, Garen Haryanyan, Emrah Yücesan, Yeşim Kesim, Çiğdem Özkara, Annapurna Poduri, Beth R. Shiedley, Catherine Shain, Russell J. Buono, Thomas N. Ferraro, Michael R. Sperling, Warren Lo, Michael Privitera, Jacqueline A. French, Steven Schachter, Ruben I. Kuzniecky, Orrin Devinsky, Manu Hegde, Pouya Khankhanian, Katherine L. Helbig, Colin A. Ellis, Gianfranco Spalletta, Fabrizio Piras, Federica Piras, Tommaso Gili, Valentina Ciullo, Andreas Reif, Andrew McQuillin, Nick Bass, Andrew McIntosh, Douglas Blackwood, Mandy Johnstone, Aarno Palotie, Michele T. Pato, Carlos N. Pato, Evelyn J. Bromet, Celia Barreto Carvalho, Eric D. Achtyes, Maria Helena Azevedo, Roman Kotov, Douglas S. Lehrer, Dolores Malaspina, Stephen R. Marder, Helena Medeiros, Christopher P. Morley, Diana O. Perkins, Janet L. Sobell, Peter F. Buckley, Fabio Macciardi, Mark H. Rapaport, James A. Knowles, Ayman H. Fanous, Steven A. McCarroll, Namrata Gupta, Stacey B. Gabriel, Mark J. Daly, Eric S. Lander, Daniel H. Lowenstein, David B. Goldstein, Holger Lerche, Samuel F. Berkovic, Benjamin M. Neale, Wellcome Trust, Department of Health, Institute of Neurology, UCL, Imperial College Healthcare NHS Trust- BRC Funding, Commission of the European Communities, Medical Research Council (MRC), Feng Y.-C.A., Howrigan D.P., Abbott L.E., Tashman K., Cerrato F., Singh T., Heyne H., Byrnes A., Churchhouse C., Watts N., Solomonson M., Lal D., Heinzen E.L., Dhindsa R.S., Stanley K.E., Cavalleri G.L., Hakonarson H., Helbig I., Krause R., May P., Weckhuysen S., Petrovski S., Kamalakaran S., Sisodiya S.M., Cossette P., Cotsapas C., De Jonghe P., Dixon-Salazar T., Guerrini R., Kwan P., Marson A.G., Stewart R., Depondt C., Dlugos D.J., Scheffer I.E., Striano P., Freyer C., McKenna K., Regan B.M., Bellows S.T., Leu C., Bennett C.A., Johns E.M.C., Macdonald A., Shilling H., Burgess R., Weckhuysen D., Bahlo M., O'Brien T.J., Todaro M., Stamberger H., Andrade D.M., Sadoway T.R., Mo K., Krestel H., Gallati S., Papacostas S.S., Kousiappa I., Tanteles G.A., Sterbova K., Vlckova M., Sedlackova L., Lassuthova P., Klein K.M., Rosenow F., Reif P.S., Knake S., Kunz W.S., Zsurka G., Elger C.E., Bauer J., Rademacher M., Pendziwiat M., Muhle H., Rademacher A., van Baalen A., von Spiczak S., Stephani U., Afawi Z., Korczyn A.D., Kanaan M., Canavati C., Kurlemann G., Muller-Schluter K., Kluger G., Hausler M., Blatt I., Lemke J.R., Krey I., Weber Y.G., Wolking S., Becker F., Hengsbach C., Rau S., Maisch A.F., Steinhoff B.J., Schulze-Bonhage A., Schubert-Bast S., Schreiber H., Borggrafe I., Schankin C.J., Mayer T., Korinthenberg R., Brockmann K., Dennig D., Madeleyn R., Kalviainen R., Auvinen P., Saarela A., Linnankivi T., Lehesjoki A.-E., Rees M.I., Chung S.-K., Pickrell W.O., Powell R., Schneider N., Balestrini S., Zagaglia S., Braatz V., Johnson M.R., Auce P., Sills G.J., Baum L.W., Sham P.C., Cherny S.S., Lui C.H.T., Barisic N., Delanty N., Doherty C.P., Shukralla A., McCormack M., El-Naggar H., Canafoglia L., Franceschetti S., Castellotti B., Granata T., Zara F., Iacomino M., Madia F., Vari M.S., Mancardi M.M., Salpietro V., Bisulli F., Tinuper P., Licchetta L., Pippucci T., Stipa C., Minardi R., Gambardella A., Labate A., Annesi G., Manna L., Gagliardi M., Parrini E., Mei D., Vetro A., Bianchini C., Montomoli M., Doccini V., Marini C., Suzuki T., Inoue Y., Yamakawa K., Tumiene B., Sadleir L.G., King C., Mountier E., Caglayan S.H., Arslan M., Yapici Z., Yis U., Topaloglu P., Kara B., Turkdogan D., Gundogdu-Eken A., Bebek N., Ugur-Iseri S., Baykan B., Salman B., Haryanyan G., Yucesan E., Kesim Y., Ozkara C., Poduri A., Shiedley B.R., Shain C., Buono R.J., Ferraro T.N., Sperling M.R., Lo W., Privitera M., French J.A., Schachter S., Kuzniecky R.I., Devinsky O., Hegde M., Khankhanian P., Helbig K.L., Ellis C.A., Spalletta G., Piras F., Gili T., Ciullo V., Reif A., McQuillin A., Bass N., McIntosh A., Blackwood D., Johnstone M., Palotie A., Pato M.T., Pato C.N., Bromet E.J., Carvalho C.B., Achtyes E.D., Azevedo M.H., Kotov R., Lehrer D.S., Malaspina D., Marder S.R., Medeiros H., Morley C.P., Perkins D.O., Sobell J.L., Buckley P.F., Macciardi F., Rapaport M.H., Knowles J.A., Fanous A.H., McCarroll S.A., Gupta N., Gabriel S.B., Daly M.J., Lander E.S., Lowenstein D.H., Goldstein D.B., Lerche H., Berkovic S.F., Neale B.M., Epi25 Collaborative, YÜCESAN, EMRAH, Institute for Molecular Medicine Finland, Children's Hospital, HUS Children and Adolescents, Department of Medical and Clinical Genetics, University Management, Centre of Excellence in Complex Disease Genetics, Aarno Palotie / Principal Investigator, and Genomics of Neurological and Neuropsychiatric Disorders

Subjects
s.berkovic@unimelb.edu.au [Epi25 Collaborative. Electronic address], 0301 basic medicine, GAMMA-2-SUBUNIT, burden analysi, DNA Mutational Analysis, PROTEIN, Neurodegenerative, VARIANTS, SUSCEPTIBILITY, Medical and Health Sciences, Epilepsy, 0302 clinical medicine, 2.1 Biological and endogenous factors, EPIDEMIOLOGY, Missense mutation, Exome, Aetiology, Genetics (clinical), Exome sequencing, 11 Medical and Health Sciences, seizures, GABRG2, Genetics, Genetics & Heredity, 0303 health sciences, biology, COMMON EPILEPSIES, 1184 Genetics, developmental biology, physiology, sequencing, Biological Sciences, Epi25 Collaborative, Phenotype, GENOME, epileptic encephalopathy, burden analysis, Neurological, Biotechnology, Genetic Markers, seizure, EEF1A2, Burden analysis, epilepsy, exome, Article, 03 medical and health sciences, Clinical Research, Exome Sequencing, Genetic variation, medicine, Humans, Genetic Predisposition to Disease, Gene, EPILEPTIC SEIZURES, METAANALYSIS, 030304 developmental biology, Human Genome, Neurosciences, Genetic Variation, 06 Biological Sciences, medicine.disease, Brain Disorders, 030104 developmental biology, Genetic marker, DE-NOVO MUTATIONS, Case-Control Studies, biology.protein, 3111 Biomedicine, Human medicine, 030217 neurology & neurosurgery
Abstract

Sequencing-based studies have identified novel risk genes for rare, severe epilepsies and revealed a role of rare deleterious variation in common epilepsies. To identify the shared and distinct ultra-rare genetic risk factors for rare and common epilepsies, we performed a whole-exome sequencing (WES) analysis of 9,170 epilepsy-affected individuals and 8,364 controls of European ancestry. We focused on three phenotypic groups; the rare but severe developmental and epileptic encephalopathies (DEE), and the commoner phenotypes of genetic generalized epilepsy (GGE) and non-acquired focal epilepsy (NAFE). We observed that compared to controls, individuals with any type of epilepsy carried an excess of ultra-rare, deleterious variants in constrained genes and in genes previously associated with epilepsy, with the strongest enrichment seen in DEE and the least in NAFE. Moreover, we found that inhibitory GABAA receptor genes were enriched for missense variants across all three classes of epilepsy, while no enrichment was seen in excitatory receptor genes. The larger gene groups for the GABAergic pathway or cation channels also showed a significant mutational burden in DEE and GGE. Although no single gene surpassed exome-wide significance among individuals with GGE or NAFE, highly constrained genes and genes encoding ion channels were among the top associations, including CACNA1G, EEF1A2, and GABRG2 for GGE and LGI1, TRIM3, and GABRG2 for NAFE. Our study confirms a convergence in the genetics of common and rare epilepsies associated with ultra-rare coding variation and highlights a ubiquitous role for GABAergic inhibition in epilepsy etiology in the largest epilepsy WES study to date.

Published
2019
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14. Exome-based analysis of cardiac arrhythmia, respiratory control, and epilepsy genes in sudden unexpected death in epilepsy

Author

Richard D. Bagnall, Slavé Petrovski, Lien Lam, Anita Cairns, Zaid Afawi, Leanne M. Dibbens, Douglas E. Crompton, Christopher Semsarian, Sarah I. Garry, Carina Cutmore, Brigid M. Regan, Johan Duflou, Samuel F. Berkovic, Ingrid E. Scheffer, Lynette G. Sadleir, and Sara Kivity

Subjects
0301 basic medicine, medicine.medical_specialty, medicine.diagnostic_test, business.industry, Cardiac arrhythmia, Gene mutation, medicine.disease, Bioinformatics, 03 medical and health sciences, Epilepsy, 030104 developmental biology, 0302 clinical medicine, Neurology, Dravet syndrome, Internal medicine, medicine, Cardiology, Neurology (clinical), Generalized epilepsy, business, Exome, 030217 neurology & neurosurgery, Exome sequencing, Genetic testing
Abstract

Objective The leading cause of epilepsy-related premature mortality is sudden unexpected death in epilepsy (SUDEP). The cause of SUDEP remains unknown. To search for genetic risk factors in SUDEP cases, we performed an exome-based analysis of rare variants. Methods Demographic and clinical information of 61 SUDEP cases were collected. Exome sequencing and rare variant collapsing analysis with 2,936 control exomes were performed to test for genes enriched with damaging variants. Additionally, cardiac arrhythmia, respiratory control, and epilepsy genes were screened for variants with frequency of

Published
2016
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15. Aberrant Inclusion of a Poison Exon Causes Dravet Syndrome and Related SCN1A-Associated Genetic Epilepsies

Author

Gemma L. Carvill, Krysta L. Engel, Aishwarya Ramamurthy, J. Nicholas Cochran, Jolien Roovers, Hannah Stamberger, Nicholas Lim, Amy L. Schneider, Georgie Hollingsworth, Dylan H. Holder, Brigid M. Regan, James Lawlor, Lieven Lagae, Berten Ceulemans, E. Martina Bebin, John Nguyen, Gregory S. Barsh, Sarah Weckhuysen, Miriam Meisler, Samuel F. Berkovic, Peter De Jonghe, Ingrid E. Scheffer, Richard M. Myers, Gregory M. Cooper, Heather C. Mefford, Pasquale Striano, Federico Zara, Ingo Helbig, Rikke S. Møller, Sarah von Spiczak, Hiltrud Muhle, Hande Caglayan, Katalin Sterbova, Dana Craiu, Dorota Hoffman, Anna-Elina Lehesjoki, Kaja Selmer, Christel Depienne, Johannes Lemke, Carla Marini, Renzo Guerrini, Bernd Neubauer, Tiina Talvik, Eric Leguern, Peter de Jonghe, and EuroEPINOMICS Rare Epilepsy Syndro

Subjects
0301 basic medicine, Male, SPLICE VARIANTS, PROTEIN, Epilepsies, Myoclonic, Sodium Channels, Transcriptome, Epilepsy, Exon, poison exon, 0302 clinical medicine, SCN1A, NEURONAL SODIUM-CHANNEL, BRAIN, Child, Genetics (clinical), Exome sequencing, Genetics, Genetics & Heredity, noncoding, Exons, Middle Aged, genome sequencing, Female, REGULATOR, Life Sciences & Biomedicine, Adult, Biology, 03 medical and health sciences, alternative splicing, Dravet syndrome, Report, medicine, Humans, Gene, Science & Technology, variant interpretation, Alternative splicing, epilepsy, Genetic Variation, medicine.disease, NAV1.1 Voltage-Gated Sodium Channel, 030104 developmental biology, DE-NOVO MUTATIONS, Neurodevelopmental Disorders, Human genome, Human medicine, 030217 neurology & neurosurgery
Abstract

Developmental and epileptic encephalopathies (DEEs) are a group of severe epilepsies characterized by refractory seizures and developmental impairment. Sequencing approaches have identified causal genetic variants in only about 50% of individuals with DEEs.1-3 This suggests that unknown genetic etiologies exist, potentially in the ∼98% of human genomes not covered by exome sequencing (ES). Here we describe seven likely pathogenic variants in regions outside of the annotated coding exons of the most frequently implicated epilepsy gene, SCN1A, encoding the alpha-1 sodium channel subunit. We provide evidence that five of these variants promote inclusion of a "poison" exon that leads to reduced amounts of full-length SCN1A protein. This mechanism is likely to be broadly relevant to human disease; transcriptome studies have revealed hundreds of poison exons,4,5 including some present within genes encoding other sodium channels and in genes involved in neurodevelopment more broadly.6 Future research on the mechanisms that govern neuronal-specific splicing behavior might allow researchers to co-opt this system for RNA therapeutics. ispartof: AMERICAN JOURNAL OF HUMAN GENETICS vol:103 issue:6 pages:1022-1029 ispartof: location:United States status: published

Published
2018
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16. Prevalence of Pathogenic Copy Number Variation in Adults With Pediatric-Onset Epilepsy and Intellectual Disability

Author

Brigid M. Regan, Anne S. Bassett, D James Stavropoulos, Danielle M. Andrade, and Felippe Borlot

Subjects
0301 basic medicine, Proband, Adult, Male, congenital, hereditary, and neonatal diseases and abnormalities, medicine.medical_specialty, Pediatrics, Adolescent, DNA Copy Number Variations, 03 medical and health sciences, Epilepsy, Young Adult, 0302 clinical medicine, Intellectual Disability, Intellectual disability, Prevalence, Medicine, Outpatient clinic, Humans, Copy-number variation, Age of Onset, Psychiatry, Original Investigation, Ontario, business.industry, Jeavons syndrome, medicine.disease, Microarray Analysis, Pedigree, 030104 developmental biology, Cross-Sectional Studies, Medical genetics, Female, Neurology (clinical), Age of onset, business, 030217 neurology & neurosurgery
Abstract

Importance Copy number variation (CNV) is an important cause of neuropsychiatric disorders. Little is known about the role of CNV in adults with epilepsy and intellectual disability. Objectives To evaluate the prevalence of pathogenic CNVs and identify possible candidate CNVs and genes in patients with epilepsy and intellectual disability. Design, Setting, and Participants In this cross-sectional study, genome-wide microarray was used to evaluate a cohort of 143 adults with unexplained childhood-onset epilepsy and intellectual disability who were recruited from the Toronto Western Hospital epilepsy outpatient clinic from January 1, 2012, through December 31, 2014. The inclusion criteria were (1) pediatric seizure onset with ongoing seizure activity in adulthood, (2) intellectual disability of any degree, and (3) no structural brain abnormalities or metabolic conditions that could explain the seizures. Main Outcomes and Measures DNA screening was performed using genome-wide microarray platforms. Pathogenicity of CNVs was assessed based on the American College of Medical Genetics guidelines. The Residual Variation Intolerance Score was used to evaluate genes within the identified CNVs that could play a role in each patient’s phenotype. Results Of the 2335 patients, 143 probands were investigated (mean [SD] age, 24.6 [10.8] years; 69 male and 74 female). Twenty-three probands (16.1%) and 4 affected relatives (2.8%) (mean [SD] age, 24.1 [6.1] years; 11 male and 16 female) presented with pathogenic or likely pathogenic CNVs (0.08-18.9 Mb). Five of the 23 probands with positive results (21.7%) had more than 1 CNV reported. Parental testing revealed de novo CNVs in 11 (47.8%), with CNVs inherited from a parent in 4 probands (17.4%). Sixteen of 23 probands (69.6%) presented with previously cataloged human genetic disorders and/or defined CNV hot spots in epilepsy. Eight nonrecurrent rare CNVs that overlapped 1 or more genes associated with intellectual disability, autism, and/or epilepsy were identified: 2p16.1-p15 duplication, 6p25.3-p25.1 duplication, 8p23.3p23.1 deletion, 9p24.3-p23 deletion, 10q11.22-q11.23 duplication, 12p13.33-13.2 duplication, 13q34 deletion, and 16p13.2 duplication. Five genes are of particular interest given their potential pathogenicity in the corresponding phenotypes and least tolerability to variation:ABAT, KIAA2022,COL4A1, CACNA1C,andSMARCA2.ABATduplication was associated with Lennox-Gastaut syndrome andKIAA2022deletion with Jeavons syndrome. Conclusions and Relevance The high prevalence of pathogenic CNVs in this study highlights the importance of microarray analysis in adults with unexplained childhood-onset epilepsy and intellectual disability. Additional studies and comparison with similar cases are required to evaluate the effects of deletions and duplications that overlap specific genes.

Published
2017

17. Ultra-rare genetic variation in common epilepsies: a case-control sequencing study

Author

Andrew S Allen, Susannah T Bellows, Samuel F Berkovic, Joshua Bridgers, Rosemary Burgess, Gianpiero Cavalleri, Seo-Kyung Chung, Patrick Cossette, Norman Delanty, Dennis Dlugos, Michael P Epstein, Catharine Freyer, David B Goldstein, Erin L Heinzen, Michael S Hildebrand, Michael R Johnson, Ruben Kuzniecky, Daniel H Lowenstein, Anthony G Marson, Richard Mayeux, Caroline Mebane, Heather C Mefford, Terence J O'Brien, Ruth Ottman, Steven Petrou, Slavgé Petrovski, William O Pickrell, Annapurna Poduri, Rodney A Radtke, Mark I Rees, Brigid M Regan, Zhong Ren, Ingrid E Scheffer, Graeme J Sills, Rhys H Thomas, Quanli Wang, Bassel Abou-Khalil, Brian K Alldredge, Dina Amrom, Eva Andermann, Frederick Andermann, Jocelyn F. Bautista, Judith Bluvstein, Alex Boro, Gregory D Cascino, Damian Consalvo, Patricia Crumrine, Orrin Devinsky, Miguel Fiol, Nathan B Fountain, Jacqueline French, Daniel Friedman, Eric B Geller, Tracy Glauser, Simon Glynn, Kevin Haas, Sheryl R Haut, Jean Hayward, Sandra L Helmers, Sucheta Joshi, Andres Kanner, Heidi E Kirsch, Robert C Knowlton, Eric H Kossoff, Rachel Kuperman, Paul V Motika, Edward J Novotny, Juliann M Paolicchi, Jack M Parent, Kristen Park, Lynette G Sadleir, Renée A. Shellhaas, Elliott H Sherr, Jerry J. Shih, Shlomo Shinnar, Rani K Singh, Joseph Sirven, Michael C Smith, Joseph Sullivan, Liu Lin Thio, Anu Venkat, Eileen P.G Vining, Gretchen K Von Allmen, Judith L Weisenberg, Peter Widdess-Walsh, Melodie R Winawer, and Imperial College Healthcare NHS Trust- BRC Funding

Subjects
0301 basic medicine, medicine.medical_specialty, Population, Disease, Bioinformatics, 03 medical and health sciences, Epilepsy, 0302 clinical medicine, Epilepsy Phenome/Genome Project, Genetic variation, medicine, Humans, Exome, Genetic Predisposition to Disease, education, Psychiatry, education.field_of_study, Neurology & Neurosurgery, business.industry, Genetic Variation, 1103 Clinical Sciences, Sequence Analysis, DNA, medicine.disease, Comorbidity, R1, 030104 developmental biology, Case-Control Studies, Epilepsy syndromes, Epilepsy, Generalized, Epilepsies, Partial, Neurology (clinical), 1109 Neurosciences, business, 030217 neurology & neurosurgery
Abstract

Summary Background Despite progress in understanding the genetics of rare epilepsies, the more common epilepsies have proven less amenable to traditional gene-discovery analyses. We aimed to assess the contribution of ultra-rare genetic variation to common epilepsies. Methods We did a case-control sequencing study with exome sequence data from unrelated individuals clinically evaluated for one of the two most common epilepsy syndromes: familial genetic generalised epilepsy, or familial or sporadic non-acquired focal epilepsy. Individuals of any age were recruited between Nov 26, 2007, and Aug 2, 2013, through the multicentre Epilepsy Phenome/Genome Project and Epi4K collaborations, and samples were sequenced at the Institute for Genomic Medicine (New York, USA) between Feb 6, 2013, and Aug 18, 2015. To identify epilepsy risk signals, we tested all protein-coding genes for an excess of ultra-rare genetic variation among the cases, compared with control samples with no known epilepsy or epilepsy comorbidity sequenced through unrelated studies. Findings We separately compared the sequence data from 640 individuals with familial genetic generalised epilepsy and 525 individuals with familial non-acquired focal epilepsy to the same group of 3877 controls, and found significantly higher rates of ultra-rare deleterious variation in genes established as causative for dominant epilepsy disorders (familial genetic generalised epilepsy: odd ratio [OR] 2·3, 95% CI 1·7–3·2, p=9·1 × 10 −8 ; familial non-acquired focal epilepsy 3·6, 2·7–4·9, p=1·1 × 10 −17 ). Comparison of an additional cohort of 662 individuals with sporadic non-acquired focal epilepsy to controls did not identify study-wide significant signals. For the individuals with familial non-acquired focal epilepsy, we found that five known epilepsy genes ranked as the top five genes enriched for ultra-rare deleterious variation. After accounting for the control carrier rate, we estimate that these five genes contribute to the risk of epilepsy in approximately 8% of individuals with familial non-acquired focal epilepsy. Our analyses showed that no individual gene was significantly associated with familial genetic generalised epilepsy; however, known epilepsy genes had lower p values relative to the rest of the protein-coding genes (p=5·8 × 10 −8 ) that were lower than expected from a random sampling of genes. Interpretation We identified excess ultra-rare variation in known epilepsy genes, which establishes a clear connection between the genetics of common and rare, severe epilepsies, and shows that the variants responsible for epilepsy risk are exceptionally rare in the general population. Our results suggest that the emerging paradigm of targeting of treatments to the genetic cause in rare devastating epilepsies might also extend to a proportion of common epilepsies. These findings might allow clinicians to broadly explain the cause of these syndromes to patients, and lay the foundation for possible precision treatments in the future. Funding National Institute of Neurological Disorders and Stroke (NINDS), and Epilepsy Research UK.

Published
2017

18. High Rate of Recurrent De Novo Mutations in Developmental and Epileptic Encephalopathies

Author

Patrick Cossette, Zoha Kibar, Maxime Cadieux-Dion, Helen Brittain, Andrew E. Fry, Emily Fassi, Edward Blair, Simone Martinelli, Paul J. Benke, Guy D'Anjou, Alexandre D. Laporte, Berge A. Minassian, Sylvia Stockler, Tyson L Ware, David R. FitzPatrick, Weimin Bi, Amy L Schneider, Jill A. Rosenfeld, Shekeeb S. Mohammad, Jacques L. Michaud, Carlos A. Bacino, Joss Shelagh, Samuel F. Berkovic, Stéphane Auvin, Yunru Shao, Sylvia Dobrzeniecka, Kelly Mo, Cory Tam, Nicole Corsten-Janssen, Wendy K. Chung, Renee-Myriam Boucher, Alain Verloes, Fadi F. Hamdan, Bronwyn Kerr, Frédéric Tran Mau-Them, Martina Bebin, Philippe M. Campeau, Dara V.F. Albert, Guy A. Rouleau, Quinn Stein, Anne Lortie, Susan M. Hiatt, Lubov Blumkin, Boris Keren, Dan Spiegelman, Saadet Mercimek-Mahmutoglu, Ronald G. Lafrenière, Marie-Christine Nougues, Rhys H. Thomas, Erica H. Gerkes, Elsa Rossignol, Bruno Dallapiccola, Klaas J. Wierenga, Natalie Canham, Monica H. Wojcik, Caroline Meloche, Moira Blyth, Cyril Mignot, Heather C Mefford, Ledia Brunga, D. L. Jones, François Dubeau, Kyle Retterer, James J. O'Byrne, Christine Massicotte, Vincenzo Leuzzi, Caroline Nava, Ingrid E. Scheffer, Erik-Jan Kamsteeg, Cyrus Boelman, Megan T. Cho, Gabriela Purcarin, Brigid M. Regan, Jean Monlong, Simon Girard, Philippe Major, Marguerite Miguet, Katrin Õunap, Yu Chi Liu, Guillaume Bourque, Myriam Srour, Ousmane Diallo, Emilie Riou, Lionel Carmant, Seema R. Lalani, Christina Nassif, Robert Roger Lebel, Anna Lehman, Georgie Hollingsworth, Stéphanie Jacques, Sunita Venkateswaran, Marco Tartaglia, Candace T. Myers, Ange-Line Bruel, Danielle M. Andrade, Imad Jarjour, Peyman Bizargity, Sara J. Dorison, Jane A. Hurst, Richard E. Frye, Lynette G. Sadleir, Alan Donaldson, Fernando Scaglia, Philippe Lemay, Paola Diadori, Laura Davis-Keppen, Division of Genetic Medicine [Seattle], University of Washington [Seattle], Centre hospitalier universtaire de Montréal, Université de Montréal, Baylor College of Medicine ( BCM ), Baylor College of Medicine, Laboratoire de Diagnostic Génétique, CHU Strasbourg-Hopital Civil, Clinical Genetics Department, St Michael's Hospital, Department of Clinical Genetics, Oxford Regional Genetics Service, The Churchill hospital, Regional Genetic Service, St Mary's Hospital, Manchester, SUNY Upstate Medical University, Centre de génétique - Centre de référence des maladies rares, anomalies du développement et syndromes malformatifs (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand ( CHU Dijon ), Equipe GAD (LNC - U1231), Lipides - Nutrition - Cancer [Dijon - U1231] ( LNC ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Hôpital Robert Debré, Universitätsklinikum Leipzig, Institute of Plant and Microbial Biology, Academia Sinica, Istituto di Genetica Medica, Medical Genetics and Pediatric Cardiology, IRCCS Ospedale Pediatrico Bambino Gesù [Roma], Ematologia, Oncologia e Medicina Molecolare, Istituto Superiore di Sanita', Service de Génétique Cytogénétique et Embryologie [CHU Pitié-Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP)-CHU Pitié-Salpêtrière [APHP], Service de génétique, cytogénétique, embryologie [Pitié-Salpétrière], Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Assistance publique - Hôpitaux de Paris (AP-HP)-CHU Pitié-Salpêtrière [APHP], 'Personal Protection Against Vectors' working group ( PPAV ), PPAV working group, Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute ( ICM ), Centre National de la Recherche Scientifique ( CNRS ) -CHU Pitié-Salpêtrière [APHP]-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ), Département de Mathématiques, Université de Sherbrooke, Université de Sherbrooke [Sherbrooke], McGill University and Genome Quebec Innovation Centre, Center of Excellence in Neuromics, University of Montreal, The Hospital for sick children [Toronto] ( SickKids ), CHU Sainte Justine [Montréal], Genome Canada Genome Quebec Jeanne and Jean-Louis Levesque Foundation Michael Bahen Chair in Epilepsy Research Ontario Brain Institute McLaughlin Foundation University of Toronto National Institute of Neurological Disorders and Stroke RO1 NS069605 University of Toronto McLaughlin Accelerator Grant in Genomic Medicine MC-2013-08, Baylor College of Medicine (BCM), Baylor University, State University of New York (SUNY), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Istituto Superiore di Sanità (ISS), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), 'Personal Protection Against Vectors' working group (PPAV), Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Département de mathématiques [Sherbrooke] (UdeS), Faculté des sciences [Sherbrooke] (UdeS), Université de Sherbrooke (UdeS)-Université de Sherbrooke (UdeS), The Hospital for sick children [Toronto] (SickKids), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Université Pierre et Marie Curie - Paris 6 (UPMC)

Subjects
Male, 0301 basic medicine, Candidate gene, medicine.medical_specialty, medical genetics, glycosylation, Nonsense mutation, Genome-wide association study, Gene mutation, Biology, Sensory disorders Donders Center for Medical Neuroscience [Radboudumc 12], Article, severe intellectual disability, 03 medical and health sciences, Epilepsy, 0302 clinical medicine, children, Recurrence, Seizures, Genetic linkage, Intellectual Disability, [ SDV.MHEP ] Life Sciences [q-bio]/Human health and pathology, Journal Article, Genetics, medicine, Humans, Child, disorders, Genetics (clinical), Genetic association, Brain Diseases, disease, cis-prenyltransferase, Genome, Human, structural basis, medicine.disease, diphosphate synthase, 030104 developmental biology, Child, Preschool, Mutation, Medical genetics, Female, nogo-b receptor, 030217 neurology & neurosurgery, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Genome-Wide Association Study, Meta-Analysis
Abstract

Item does not contain fulltext Developmental and epileptic encephalopathy (DEE) is a group of conditions characterized by the co-occurrence of epilepsy and intellectual disability (ID), typically with developmental plateauing or regression associated with frequent epileptiform activity. The cause of DEE remains unknown in the majority of cases. We performed whole-genome sequencing (WGS) in 197 individuals with unexplained DEE and pharmaco-resistant seizures and in their unaffected parents. We focused our attention on de novo mutations (DNMs) and identified candidate genes containing such variants. We sought to identify additional subjects with DNMs in these genes by performing targeted sequencing in another series of individuals with DEE and by mining various sequencing datasets. We also performed meta-analyses to document enrichment of DNMs in candidate genes by leveraging our WGS dataset with those of several DEE and ID series. By combining these strategies, we were able to provide a causal link between DEE and the following genes: NTRK2, GABRB2, CLTC, DHDDS, NUS1, RAB11A, GABBR2, and SNAP25. Overall, we established a molecular diagnosis in 63/197 (32%) individuals in our WGS series. The main cause of DEE in these individuals was de novo point mutations (53/63 solved cases), followed by inherited mutations (6/63 solved cases) and de novo CNVs (4/63 solved cases). De novo missense variants explained a larger proportion of individuals in our series than in other series that were primarily ascertained because of ID. Moreover, these DNMs were more frequently recurrent than those identified in ID series. These observations indicate that the genetic landscape of DEE might be different from that of ID without epilepsy.

Published
2017
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19. Mutations in mammalian target of rapamycin regulatorDEPDC5cause focal epilepsy with brain malformations

Author

Federica Provini, Samuel F. Berkovic, Francesca Bisulli, Laura Licchetta, Ingrid E. Scheffer, Paolo Tinuper, Leanne M. Dibbens, Michael G. Ricos, Sarah E. Heron, Bree L. Hodgson, Douglas E. Crompton, Simone Mandelstam, Brigid M. Regan, Lata Vadlamudi, Alan Connelly, and Jozef Gecz

Subjects
Pathology, medicine.medical_specialty, Mutation, Biology, medicine.disease, NPRL3, medicine.disease_cause, DEPDC5, Phenotype, Tuberous sclerosis, Epilepsy, Neurology, Cancer research, medicine, TOR Serine-Threonine Kinases, Neurology (clinical), PI3K/AKT/mTOR pathway
Abstract

We recently identified DEPDC5 as the gene for familial focal epilepsy with variable foci and found mutations in >10% of small families with nonlesional focal epilepsy. Here we show that DEPDC5 mutations are associated with both lesional and nonlesional epilepsies, even within the same family. DEPDC5-associated malformations include bottom-of-the-sulcus dysplasia (3 members from 2 families), and focal band heterotopia (1 individual). DEPDC5 negatively regulates the mammalian target of rapamycin (mTOR) pathway, which plays a key role in cell growth. The clinicoradiological phenotypes associated with DEPDC5 mutations share features with the archetypal mTORopathy, tuberous sclerosis, raising the possibility of therapies targeted to this pathway.

Published
2014
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20. GRIN2A mutations cause epilepsy-aphasia spectrum disorders

Author

John A. Damiano, Eileen Geraghty, Gemma L. Carvill, Heather C Mefford, Samantha J. Turner, Adiba Khan, Robert A. Ouvrier, Ingrid E. Scheffer, Meng-Han Tsai, Jay Shendure, Samuel F. Berkovic, Brian J. O'Roak, Natalia Lozovaya, Nadine Bruneau, Michael S. Hildebrand, Brigid M. Regan, Richard Webster, Simone C. Yendle, Nail Burnashev, Pierre Szepetowski, Lynette G. Sadleir, and Joseph Cook

Subjects
Male, Proband, Landau–Kleffner syndrome, Biology, Bioinformatics, Receptors, N-Methyl-D-Aspartate, Article, 03 medical and health sciences, Epilepsy, 0302 clinical medicine, Aphasia, Genetics, medicine, Humans, 030304 developmental biology, Landau-Kleffner Syndrome, 0303 health sciences, Electroencephalography, medicine.disease, Pedigree, 3. Good health, Rolandic epilepsy, Phenotype, Mutation, Epilepsy syndromes, Etiology, Female, medicine.symptom, Developmental regression, 030217 neurology & neurosurgery
Abstract

Epilepsy-aphasia syndromes (EAS) are a group of rare, severe epileptic encephalopathies of unknown etiology with a characteristic electroencephalogram (EEG) pattern and developmental regression particularly affecting language. Rare pathogenic deletions that include GRIN2A have been implicated in neurodevelopmental disorders. We sought to delineate the pathogenic role of GRIN2A in 519 probands with epileptic encephalopathies with diverse epilepsy syndromes. We identified four probands with GRIN2A variants that segregated with the disorder in their families. Notably, all four families presented with EAS, accounting for 9% of epilepsy-aphasia cases. We did not detect pathogenic variants in GRIN2A in other epileptic encephalopathies (n = 475) nor in probands with benign childhood epilepsy with centrotemporal spikes (n = 81). We report the first monogenic cause, to our knowledge, for EAS. GRIN2A mutations are restricted to this group of cases, which has important ramifications for diagnostic testing and treatment and provides new insights into the pathogenesis of this debilitating group of conditions.

Published
2013

21. Real-world utility of whole exome sequencing with targeted gene analysis for focal epilepsy

Author

Natalie P. Thorne, Sebastian Lunke, Michael S. Hildebrand, John A. Damiano, Clara Gaff, Piero Perucca, Ingrid E. Scheffer, A. Simon Harvey, Patrick Kwan, Terence J. O'Brien, Paul A. James, Brigid M. Regan, and Samuel F. Berkovic

Subjects
0301 basic medicine, Adult, Male, medicine.medical_specialty, Pediatrics, Adolescent, 03 medical and health sciences, Epilepsy, Young Adult, 0302 clinical medicine, Intellectual disability, Exome Sequencing, medicine, Humans, Epilepsy surgery, Genetic Testing, Prospective Studies, Family history, Child, Exome sequencing, Genetic testing, Aged, medicine.diagnostic_test, business.industry, Genetic Variation, Sequence Analysis, DNA, Middle Aged, medicine.disease, DEPDC5, Surgery, Pedigree, 030104 developmental biology, Clinical research, Neurology, Child, Preschool, Female, Neurology (clinical), Epilepsies, Partial, business, 030217 neurology & neurosurgery
Abstract

Objective Driven by advances in genomic technology and reduction in costs, next-generation sequencing (NGS) is venturing into routine clinical care. The ‘real-world' clinical utility of NGS remains to be determined in focal epilepsies, which account for 60% of all epilepsies and for which the importance of genetic factors is just beginning to emerge. We investigated the diagnostic yield and management implications of whole exome sequencing (WES)-based screening of selected genes in the routine care of common focal epilepsies suspected to have a genetic basis. Methods We performed WES, followed by targeted analysis of 64 epilepsy genes, on 40 consecutive children and adults enrolled prospectively from routine clinical practice who had MRI-negative focal epilepsy and a family history of febrile seizures or any type of epilepsy in at least one first- or second-degree relative. Exclusion criteria were previous genetic testing, severe intellectual disability and benign focal epilepsies of childhood. Results 5/40 (12.5%) patients had a pathogenic or likely pathogenic variant, detected in SCN1A , DEPDC5 , PCDH19, GABRG2 or NPRL2 . Identifying a pathogenic SCN1A variant in a patient with drug-resistant epilepsy prompted to halt presurgical investigations due to concern of unfavorable post-surgical outcome. It also led in the same patient to discontinue long-standing carbamazepine therapy (a potentially aggravating drug in epilepsies due to SCN1A mutations), resulting in complete seizure control. Patients with pathogenic or likely pathogenic variants had a younger median age of seizure onset (range) compared to those without [18 months (8 months-18 years) vs 18 years (18 months-70 years), p=0.02]. Significance Our data demonstrate that WES with targeted gene analysis is an effective diagnostic tool for patients with common focal epilepsies in whom a genetic etiology is suspected. It can also influence clinical decision-making, including antiepileptic drug selection and consideration of epilepsy surgery, hence supporting its incorporation in the routine clinical care of this patient group.

Published
2016

22. Family studies of individuals with eyelid myoclonia with absences

Author

Ingrid E. Scheffer, Brigid M. Regan, Andrew Bleasel, Danya F. Vears, Natalie Redshaw, and Lynette G. Sadleir

Subjects
Proband, medicine.medical_specialty, Pediatrics, business.industry, medicine.disease, Idiopathic generalized epilepsy, Epilepsy, Absence seizure, Childhood absence epilepsy, Neurology, Epilepsy syndromes, medicine, Neurology (clinical), medicine.symptom, Juvenile myoclonic epilepsy, Psychiatry, business, Myoclonus
Abstract

Summary Purpose: Eyelid myoclonia with absences (EM) is an uncommon type of absence seizure associated with a variety of epilepsy syndromes. The syndrome of epilepsy with EM (EMA) has been proposed to denote the onset of frequent EM induced by eye closure and photic stimulation beginning in childhood. The clinical genetics of EMA has not been well characterized, although a family history of seizures is not infrequent. Methods: Individuals with EMA were ascertained by referral and through the investigators’ clinical practices. All available family members were assessed for seizures using a validated seizure questionnaire. Electroclinical data were obtained on each proband and all affected family members; pedigrees were constructed. Families were analyzed for phenotypic patterns. Key Findings: Eighteen individuals with EMA were recruited. A history of seizures was found in 34 relatives in 15 (83%) of 18 families. In terms of epilepsy syndromes, 9 relatives from 7 of 15 families had febrile seizures. Two relatives had EMA. Classical genetic generalized epilepsy (GGE) syndromes were seen in five relatives: two generalized tonic–clonic seizures alone, two childhood absence epilepsy (CAE), and one juvenile myoclonic epilepsy (JME). Genetic epilepsy with febrile seizures plus (GEFS+) phenotypes occurred in 16 relatives. On review of the epilepsy syndromes within each family, seven families had a pattern consistent with GEFS+, whereas three families had classical GGE. Significance: The clinical genetics of EMA is suggestive of complex inheritance with shared genetic determinants overlapping with both classical GGE and GEFS+. The epilepsy syndromes in relatives of probands with EMA differ from those found in families of probands with CAE, supporting the concept that patients with EMA have a syndrome that is distinct from CAE. This presumably reflects different genetic components contributing to their genetic architecture.

Published
2012
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23. Exome-based analysis of cardiac arrhythmia, respiratory control, and epilepsy genes in sudden unexpected death in epilepsy

Author

Richard D, Bagnall, Douglas E, Crompton, Slavé, Petrovski, Lien, Lam, Carina, Cutmore, Sarah I, Garry, Lynette G, Sadleir, Leanne M, Dibbens, Anita, Cairns, Sara, Kivity, Zaid, Afawi, Brigid M, Regan, Johan, Duflou, Samuel F, Berkovic, Ingrid E, Scheffer, and Christopher, Semsarian

Subjects
Adult, Male, Epilepsy, Adolescent, Infant, Arrhythmias, Cardiac, Middle Aged, Respiration Disorders, Death, Sudden, Long QT Syndrome, Young Adult, Child, Preschool, Mutation, Humans, Exome, Female, Child, Genes, Dominant
Abstract

The leading cause of epilepsy-related premature mortality is sudden unexpected death in epilepsy (SUDEP). The cause of SUDEP remains unknown. To search for genetic risk factors in SUDEP cases, we performed an exome-based analysis of rare variants.Demographic and clinical information of 61 SUDEP cases were collected. Exome sequencing and rare variant collapsing analysis with 2,936 control exomes were performed to test for genes enriched with damaging variants. Additionally, cardiac arrhythmia, respiratory control, and epilepsy genes were screened for variants with frequency of0.1% and predicted to be pathogenic with multiple in silico tools.The 61 SUDEP cases were categorized as definite SUDEP (n = 54), probable SUDEP (n = 5), and definite SUDEP plus (n = 2). We identified de novo mutations, previously reported pathogenic mutations, or candidate pathogenic variants in 28 of 61 (46%) cases. Four SUDEP cases (7%) had mutations in common genes responsible for the cardiac arrhythmia disease, long QT syndrome (LQTS). Nine cases (15%) had candidate pathogenic variants in dominant cardiac arrhythmia genes. Fifteen cases (25%) had mutations or candidate pathogenic variants in dominant epilepsy genes. No gene reached genome-wide significance with rare variant collapsing analysis; however, DEPDC5 (p = 0.00015) and KCNH2 (p = 0.0037) were among the top 30 genes, genome-wide.A sizeable proportion of SUDEP cases have clinically relevant mutations in cardiac arrhythmia and epilepsy genes. In cases with an LQTS gene mutation, SUDEP may occur as a result of a predictable and preventable cause. Understanding the genetic basis of SUDEP may inform cascade testing of at-risk family members.

Published
2015

24. PRIMA1 mutation: a new cause of nocturnal frontal lobe epilepsy

Author

Antonio Gambardella, Brigid M. Regan, Aiden Eliot Shearer, Samuel F. Berkovic, Francesca Bisulli, Sara Baldassari, Carla Marini, Renzo Guerrini, Hans Henrik M. Dahl, Tommaso Pippucci, Richard J.H. Smith, Ingrid E. Scheffer, Laura Lichetta, Rick M. Tankard, Christopher A. Reid, Steven Petrou, Angelo Labate, Kate M. Lawrence, Melanie Bahlo, Michael S. Hildebrand, John A. Damiano, Paolo Tinuper, Elena V. Gazina, Hildebrand M.S., Tankard R., Gazina E.V., Damiano J.A., Lawrence K.M., Dahl H-H. M., Regan B.M., Shearer A.E., Smith R.J.H., Marini C., Guerrini R., Labate A., Gambardella A., Tinuper P., Licchetta L., Baldassari S., Bisulli F., Pippucci T., Scheffer I.E., Reid C.A., Petrou S., Bahlo M., and Berkovic S.F.

Subjects
Genetics, Mutation, Splice site mutation, Autosomal recessive nocturnal frontal lobe epilepsy, General Neuroscience, Nocturnal frontal lobe epilepsy, Biology, medicine.disease_cause, PRIMA1, NFLE, Exon, Genetic linkage, intellectual disability, Autosomal Dominant, medicine, Neurology (clinical), Exome, Exome sequencing, Research Articles, Minigene
Abstract

OBJECTIVE: Nocturnal frontal lobe epilepsy (NFLE) can be sporadic or autosomal dominant; some families have nicotinic acetylcholine receptor subunit mutations. We report a novel autosomal recessive phenotype in a single family and identify the causative gene. METHODS: Whole exome sequencing data was used to map the family, thereby narrowing exome search space, and then to identify the mutation. RESULTS: Linkage analysis using exome sequence data from two affected and two unaffected subjects showed homozygous linkage peaks on chromosomes 7, 8, 13, and 14 with maximum LOD scores between 1.5 and 1.93. Exome variant filtering under these peaks revealed that the affected siblings were homozygous for a novel splice site mutation (c.93+2T>C) in the PRIMA1 gene on chromosome 14. No additional PRIMA1 mutations were found in 300 other NFLE cases. The c.93+2T>C mutation was shown to lead to skipping of the first coding exon of the PRIMA1 mRNA using a minigene system. INTERPRETATION: PRIMA1 is a transmembrane protein that anchors acetylcholinesterase (AChE), an enzyme hydrolyzing acetycholine, to membrane rafts of neurons. PRiMA knockout mice have reduction of AChE and accumulation of acetylcholine at the synapse; our minigene analysis suggests that the c.93+2T>C mutation leads to knockout of PRIMA1. Mutations with gain of function effects in acetylcholine receptor subunits cause autosomal dominant NFLE. Thus, enhanced cholinergic responses are the likely cause of the severe NFLE and intellectual disability segregating in this family, representing the first recessive case to be reported and the first PRIMA1 mutation implicated in disease.

Published
2015

25. Genetic analysis of PHOX2B in sudden unexpected death in epilepsy cases

Author

Richard D. Bagnall, Ingrid E. Scheffer, Douglas E. Crompton, Samuel F. Berkovic, Carina Cutmore, Brigid M. Regan, and Christopher Semsarian

Subjects
Adult, Male, Adolescent, Biology, Genetic analysis, Frameshift mutation, Exon, Epilepsy, Death, Sudden, Young Adult, Risk Factors, medicine, Humans, Genetic Predisposition to Disease, Allele, Child, Alleles, Sequence (medicine), Aged, Repetitive Sequences, Nucleic Acid, Sequence Deletion, Genetics, Aged, 80 and over, Homeodomain Proteins, Point mutation, Australia, Exons, Sequence Analysis, DNA, Middle Aged, medicine.disease, Female, Neurology (clinical), Trinucleotide repeat expansion, Peptides, Transcription Factors
Abstract

Objective: To determine the contribution of sequence variations in PHOX2B to sudden unexpected death in epilepsy (SUDEP). Methods: Patients who died of SUDEP were identified in 2 major Australian cohorts, the Epilepsy Genetics research program in Melbourne and postmortem cases at the Department of Forensic Medicine in Sydney. Coding exons of the PHOX2B gene were sequenced and a fluorescent sizing assay was used to measure the PHOX2B polyalanine repeat sequence. Results: Sequencing of 68 cases of SUDEP identified a 15-nucleotide deletion in the PHOX2B polyalanine repeat region in one case, a 16-year-old adolescent with focal dyscognitive seizures from age 5 years. This deletion was verified using a fluorescent sizing assay. Two synonymous variants were identified in 4 cases, but no PHOX2B polyalanine repeat expansion alleles or point mutations were found. Conclusions: The absence of PHOX2B polyalanine repeat expansion alleles or point mutations in 68 Australian cases of SUDEP, with one deletion of uncertain significance, shows that PHOX2B mutations are not a common risk factor for SUDEP.

Published
2014

26. 16p11.2 600 kb Duplications confer risk for typical and atypical Rolandic epilepsy

Author

Eva M. Reinthaler, Dennis Lal, Sebastien Lebon, Michael S. Hildebrand, Hans-Henrik M. Dahl, Brigid M. Regan, Martha Feucht, Hannelore Steinböck, Birgit Neophytou, Gabriel M. Ronen, Laurian Roche, Ursula Gruber-Sedlmayr, Julia Geldner, Edda Haberlandt, Per Hoffmann, Stefan Herms, Christian Gieger, Melanie Waldenberger, Andre Franke, Michael Wittig, Susanne Schoch, Albert J. Becker, Andreas Hahn, Katrin Männik, Mohammad R. Toliat, Georg Winterer, Holger Lerche, Peter Nürnberg, Heather Mefford, Ingrid E. Scheffer, Samuel F. Berkovic, Jacques S. Beckmann, Thomas Sander, Sebastien Jacquemont, Alexandre Reymond, Fritz Zimprich, Bernd A. Neubauer, Bernd Neubauer, Martina Mörzinger, Arvid Suls, Sarah Weckhuysen, Lieve Claes, Liesbet Deprez, Katrien Smets, Tine Van Dyck, Tine Deconinck, Peter De Jonghe, Rikke S Møller, Laura L. Klitten, Helle Hjalgrim, Kiel Campus, Ingo Helbig, Hiltrud Muhle, Philipp Ostertag, Sarah von Spiczak, Ulrich Stephani, Holger Trucks, Christian E. Elger, Ailing A. Kleefuß-Lie, Wolfram S. Kunz, Rainer Surges, Verena Gaus, Dieter Janz, Bettina Schmitz, Felix Rosenow, Karl Martin Klein, Philipp S. Reif, Wolfgang H. Oertel, Hajo M. Hamer, Felicitas Becker, Yvonne Weber, Bobby P.C. Koeleman, Carolien de Kovel, Dick Lindhout, Agnès Ameil, Joris Andrieux, Sonia Bouquillon, Odile Boute, Jeanne de Flandre, Jean Marie Cuisset, Jean-Christophe Cuvellier, Roger Salengro, Albert David, Bert de Vries, Marie-Ange Delrue, Martine Doco-Fenzy, Bridget A. Fernandez, Delphine Heron, Boris Keren, Robert Lebel, Bruno Leheup, Suzanne Lewis, Maria Antonietta Mencarelli, Cyril Mignot, Jean-Claude Minet, Alexandre Moerman, Fanny Morice-Picard, Mafalda Mucciolo, Katrin Ounap, Laurent Pasquier, Florence Petit, Francesca Ragona, Evica Rajcan-Separovic, Alessandra Renieri, Claudine Rieubland, Damien Sanlaville, Elisabeth Sarrazin, Yiping Shen, Mieke van Haelst, Anneke Vulto-van Silfhout, 16p11.2 European Consortium, EPICURE Consortium, EuroEPINOMICS Consortium, Reinthaler, EM., Zimprich, F., Feucht, M., Steinböck, H., Neophytou, B., Geldner, J., Gruber-Sedlmayr, U., Haberlandt, E., Ronen, GM., Roche, L., Lal, D., Nürnberg, P., Sander, T., Lerche, H., Neubauer, B., Mörzinger, M., Suls, A., Weckhuysen, S., Claes, L., Deprez, L., Smets, K., Van Dyck, T., Deconinck, T., De Jonghe, P., Møller, RS., Klitten, LL., Hjalgrim, H., Campus, K., Helbig, I., Muhle, H., Ostertag, P., von Spiczak, S., Stephani, U., Trucks, H., Elger, CE., Kleefuß-Lie, AA., Kunz, WS., Surges, R., Gaus, V., Janz, D., Schmitz, B., Rosenow, F., Klein, KM., Reif, PS., Oertel, WH., Hamer, HM., Becker, F., Weber, Y., Koeleman, BP., de Kovel, C., Lindhout, D., Ameil, A., Andrieux, J., Bouquillon, S., Boute, O., Cordier, MP., Cuisset, JM., Cuvellier, JC., David, A., de Vries, B., Delrue, MA., Doco-Fenzy, M., Fernandez, BA., Heron, D., Keren, B., Lebel, R., Leheup, B., Lewis, S., Mencarelli, MA., Mignot, C., Minet, JC., Moerman, A., Morice-Picard, F., Mucciolo, M., Ounap, K., Pasquier, L., Petit, F., Ragona, F., Rajcan-Separovic, E., Renieri, A., Rieubland, C., Sanlaville, D., Sarrazin, E., Shen, Y., van Haelst, M., Vulto-van Silfhout, A., and Other departments

Subjects
Male, DNA Copy Number Variations, Chromosomes, Human, Pair 22, 610 Medicine & health, Locus (genetics), Biology, Polymorphism, Single Nucleotide, Temporal lobe, Epilepsy, Gene duplication, Chromosome Duplication, Genetics, medicine, Humans, Copy-number variation, Child, Molecular Biology, Genetics (clinical), Chromosomes, Human, Pair 15, Infant, General Medicine, Odds ratio, medicine.disease, Epilepsy, Rolandic, Rolandic epilepsy, Exact test, Chromosomes, Human, Pair 1, Child, Preschool, Female, Chromosomes, Human, Pair 16
Abstract

Rolandic epilepsy (RE) is the most common idiopathic focal childhood epilepsy. Its molecular basis is largely unknown and a complex genetic etiology is assumed in the majority of affected individuals. The present study tested whether six large recurrent copy number variants at 1q21, 15q11.2, 15q13.3, 16p11.2, 16p13.11 and 22q11.2 previously associated with neurodevelopmental disorders also increase risk of RE. Our association analyses revealed a significant excess of the 600 kb genomic duplication at the 16p11.2 locus (chr16: 29.5-30.1 Mb) in 393 unrelated patients with typical (n = 339) and atypical (ARE; n = 54) RE compared with the prevalence in 65,046 European population controls (5/393 cases versus 32/65,046 controls; Fisher's exact test P = 2.83 × 10(-6), odds ratio = 26.2, 95% confidence interval: 7.9-68.2). In contrast, the 16p11.2 duplication was not detected in 1738 European epilepsy patients with either temporal lobe epilepsy (n = 330) and genetic generalized epilepsies (n = 1408), suggesting a selective enrichment of the 16p11.2 duplication in idiopathic focal childhood epilepsies (Fisher's exact test P = 2.1 × 10(-4)). In a subsequent screen among children carrying the 16p11.2 600 kb rearrangement we identified three patients with RE-spectrum epilepsies in 117 duplication carriers (2.6%) but none in 202 carriers of the reciprocal deletion. Our results suggest that the 16p11.2 duplication represents a significant genetic risk factor for typical and atypical RE.

Published
2014
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27. Mutations in mammalian target of rapamycin regulator DEPDC5 cause focal epilepsy with brain malformations

Author

Ingrid E, Scheffer, Sarah E, Heron, Brigid M, Regan, Simone, Mandelstam, Douglas E, Crompton, Bree L, Hodgson, Laura, Licchetta, Federica, Provini, Francesca, Bisulli, Lata, Vadlamudi, Jozef, Gecz, Alan, Connelly, Paolo, Tinuper, Michael G, Ricos, Samuel F, Berkovic, and Leanne M, Dibbens

Subjects
Adult, Male, Repressor Proteins, Young Adult, TOR Serine-Threonine Kinases, GTPase-Activating Proteins, Mutation, Brain, Humans, Female, Epilepsies, Partial, Child, Pedigree
Abstract

We recently identified DEPDC5 as the gene for familial focal epilepsy with variable foci and found mutations in10% of small families with nonlesional focal epilepsy. Here we show that DEPDC5 mutations are associated with both lesional and nonlesional epilepsies, even within the same family. DEPDC5-associated malformations include bottom-of-the-sulcus dysplasia (3 members from 2 families), and focal band heterotopia (1 individual). DEPDC5 negatively regulates the mammalian target of rapamycin (mTOR) pathway, which plays a key role in cell growth. The clinicoradiological phenotypes associated with DEPDC5 mutations share features with the archetypal mTORopathy, tuberous sclerosis, raising the possibility of therapies targeted to this pathway.

Published
2013

28. Mutations in DEPDC5 cause familial focal epilepsy with variable foci

Author

Satyan Chintawar, Jozef Gecz, Sarah E. Heron, Susannah T. Bellows, Simona Donatello, Bree L. Hodgson, Paul Q. Thomas, Frederick Andermann, Alison Gardner, Claudia M Weller, Rosa Guerrero-López, Oebele F. Brouwer, Samuel F. Berkovic, Karl Martin Klein, Petra M.C. Callenbach, Arn M. J. M. van den Maagdenberg, Boukje de Vries, Laura Licchetta, Ingrid E. Scheffer, Massimo Pandolfo, Sara Kivity, Patrick Cossette, José M. Serratosa, James N. Hughes, Francesca Bisulli, Mark A. Corbett, John C. Mulley, François Dubeau, Denis Crimmins, Leanne M. Dibbens, Terence J. O'Brien, Xenia Iona, Brigid M. Regan, Eva Andermann, Douglas E. Crompton, Dibbens, Leanne Michelle, De Vries, B, Donatello, S, Heron, Sarah Elizabeth, Hodgson, Bree, Iona, Xenia, Scheffer, Ingrid E, L. M. Dibben, B. d. Vrie, S. Donatello, S. E. Heron, B. L. Hodgson, S. Chintawar, D. E. Crompton, J. N. Hughe, S. T. Bellow, K. M. Klein, P. M. C, M. A. Corbett, A. E. Gardner, S. Kivity, X. Iona, B. M. Regan, C. M. Weller, D. Crimmin, T. J. O'Brien, R. Guerrero-López, J. C. Mulley, F. Dubeau, L. Licchetta, F. Bisulli, P. Cossette, P. Q. Thoma, J. Gecz, J. Serratosa, O. F. Brouwer, F. Andermann, E. Andermann, A. M. J, M. Pandolfo, S. F. Berkovic, and I. E. Scheffer

Subjects
Male, DEPDC5, Genetic Linkage, Neuronal signal transduction, genetics, Genotype, Guanine Nucleotide Exchange Factor, Fluorescent Antibody Technique, CHROMOSOME 22Q12, Cohort Studies, Mice, Epilepsy, Genotype, Guanine Nucleotide Exchange Factors, Exome, LOBE EPILEPSY, Child, Cells, Cultured, Exome sequencing, Neurons, Genetics, genetics, Humans, Infant, Male, Mice, Middle Aged, Mutation, GTPase-Activating Proteins, Middle Aged, Cultured, Child, Child, diagnosis/genetics, Exome, NPRL3, Pedigree, Child, Preschool, Female, genetics, Female, Fluorescent Antibody Technique, Genetic Linkage, Genetic Predisposition to Disease, Preschool, Cohort Studies, Computational Biology, Epilepsie, Partial, Adult, Pluripotent Stem Cells, cytology/metabolism, Pedigree, Pluripotent Stem Cell, DOMAINS, Adolescent, SUGGESTION, GENERALIZED EPILEPSY, Biology, Young Adult, cytology/metabolism, Young Adult, LINKAGE, medicine, Animals, Humans, Genetic Predisposition to Disease, Generalized epilepsy, epilepsies, COMPLEX, Computational Biology, Infant, genetics, Neuron, medicine.disease, mutations, Repressor Proteins, Case-Control Studies, Adolescent, Adult, Animals, Case-Control Studies, Cell, Mutation, CELLS, SEIZURES, Epilepsies, Partial, MEMBRANE
Abstract

The majority of epilepsies are focal in origin, with seizures emanating from one brain region. Although focal epilepsies often arise from structural brain lesions, many affected individuals have normal brain imaging. The etiology is unknown in the majority of individuals, although genetic factors are increasingly recognized. Autosomal dominant familial focal epilepsy with variable foci (FFEVF) is notable because family members have seizures originating from different cortical regions. Using exome sequencing, we detected DEPDC5 mutations in two affected families. We subsequently identified mutations in five of six additional published large families with FFEVF. Study of families with focal epilepsy that were too small for conventional clinical diagnosis with FFEVF identified DEPDC5 mutations in approximately 12% of families (10/82). This high frequency establishes DEPDC5 mutations as a common cause of familial focal epilepsies. Shared homology with G protein signaling molecules and localization in human neurons suggest a role of DEPDC5 in neuronal signal transduction. Refereed/Peer-reviewed

Published
2013

29. Epileptic spasms are a feature ofDEPDC5mTORopathy

Author

Samuel F. Berkovic, Simone Mandelstam, Douglas E. Crompton, Matthew Zemel, Gemma L. Carvill, Amy L Schneider, Jacinta M McMahon, A. Simon Harvey, Julia Saykally, Joseph Sullivan, Brigid M. Regan, Saul A. Mullen, Katherine B. Howell, Leanne M. Dibbens, Heather C Mefford, Ingrid E. Scheffer, Richard J. Leventer, Carvill, GL, Crompton, DE, Regan, BM, McMahon, JM, Saykally, J, Zemel, M, Schneider, AL, Dibbens, L, Howell, KB, Mandelstam, S, Leventer, RJ, Harvey, AS, Mullen, SA, Berkovic, SF, Sullivan, J, Scheffer, IE, and Mefford, HC

Subjects
familial focal epilepsy, epileptic spasms, Bioinformatics, DEPDC5 mutations, Article, 03 medical and health sciences, Epilepsy, spasms, 0302 clinical medicine, medicine, Family history, Genetics (clinical), 030304 developmental biology, 0303 health sciences, business.industry, Cortical dysplasia, medicine.disease, NPRL3, DEPDC5, 3. Good health, Epileptic spasms, Clinical research, Cohort, epilepsy, Neurology (clinical), business, 030217 neurology & neurosurgery
Abstract

usc Refereed/Peer-reviewed Objective: To assess the presence of DEPDC5 mutations in a cohort of patients with epileptic spasms. Methods: We performed DEPDC5 resequencing in 130 patients with spasms, segregation analysis of variants of interest, and detailed clinical assessment of patients with possibly and likely pathogenic variants. Results: We identified 3 patients with variants in DEPDC5 in the cohort of 130 patients with spasms. We also describe 3 additional patients with DEPDC5 alterations and epileptic spasms: 2 from a previously described family and a third ascertained by clinical testing. Overall, we describe 6 patients from 5 families with spasms and DEPDC5 variants; 2 arose de novo and 3 were familial. Two individuals had focal cortical dysplasia. Clinical outcome was highly variable. Conclusions: While recent molecular findings in epileptic spasms emphasize the contribution of de novo mutations, we highlight the relevance of inherited mutations in the setting of a family history of focal epilepsies. We also illustrate the utility of clinical diagnostic testing and detailed phenotypic evaluation in characterizing the constellation of phenotypes associated with DEPDC5 alterations. We expand this phenotypic spectrum to include epileptic spasms, aligning DEPDC5 epilepsies more with the recognized features of other mTORopathies.

Published
2015
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