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1. Consistency of parent-report SLC6A1 data in Simons Searchlight with Provider-Based Publications

Author: Jennifer M. Bain, LeeAnne Green Snyder, Katherine L. Helbig, Dominique D. Cooper, Wendy K. Chung, and Kimberly Goodspeed
Subjects: SLC6A1, Neurodevelopmental disorder, Intellectual disability, Genetic, Epilepsy, Autism, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571
Abstract: Abstract Background SLC6A1-related disorder is a recently identified, rare, genetic neurodevelopmental disorder that is associated with loss-of-function variants in SLC6A1. This gene encodes GABA transporter type I that is responsible for re-uptake of GABA from the synapse into the pre-synaptic terminal or circulating neuroglia. Based upon retrospective review of published cases and available research databases including Epi25 collective and SLC6A1 Connect patient database, the phenotypic spectrum is broad and includes developmental delay, epilepsy, and autism or autistic traits. SLC6A1 is one of the genes included in the Simons Searchlight registry, which includes standardized data collection across genetically identified neurodevelopmental conditions. Methods In this study, we compare parent-report measures of phenotypic features in the Simons Searchlight registry to previously published, provider-reported cases to assess if parent-report measures are consistent with what has been reported in the literature. Results There were 116 participants in the provider-reported dataset compared to 43 individuals in the caregiver-reported dataset. Carriers in Searchlight had 83 unique pathogenic or likely pathogenic variants in SLC6A1, which were predominantly missense or nonsense variants. There was no significant difference between groups for the prevalence of developmental delay, ASD, or ADHD. Caregivers more often reported hypotonia, while epilepsy was slightly more frequently reported by providers. Conclusions We propose that standardized parent-report data collection methods are consistent with provider reports on many core features of SLC6A1-related disorder. The availability of patient registries and standardized natural history studies may fill an important need in clinical trial readiness programs, with larger sample sizes than smaller published case series.
Published: 2022
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2. High-throughput evaluation of epilepsy-associated KCNQ2 variants reveals functional and pharmacological heterogeneity

Author: Carlos G. Vanoye, Reshma R. Desai, Zhigang Ji, Sneha Adusumilli, Nirvani Jairam, Nora Ghabra, Nishtha Joshi, Eryn Fitch, Katherine L. Helbig, Dianalee McKnight, Amanda S. Lindy, Fanggeng Zou, Ingo Helbig, Edward C. Cooper, and Alfred L. George Jr.
Subjects: Genetics, Neuroscience, Medicine
Abstract: Hundreds of genetic variants in KCNQ2 encoding the voltage-gated potassium channel KV7.2 are associated with early onset epilepsy and/or developmental disability, but the functional consequences of most variants are unknown. Absent functional annotation for KCNQ2 variants hinders identification of individuals who may benefit from emerging precision therapies. We employed automated patch clamp recordings to assess at, to our knowledge, an unprecedented scale the functional and pharmacological properties of 79 missense and 2 inframe deletion KCNQ2 variants. Among the variants we studied were 18 known pathogenic variants, 24 mostly rare population variants, and 39 disease-associated variants with unclear functional effects. We analyzed electrophysiological data recorded from 9,480 cells. The functional properties of 18 known pathogenic variants largely matched previously published results and validated automated patch clamp for this purpose. Unlike rare population variants, most disease-associated KCNQ2 variants exhibited prominent loss-of-function with dominant-negative effects, providing strong evidence in support of pathogenicity. All variants responded to retigabine, although there were substantial differences in maximal responses. Our study demonstrated that dominant-negative loss-of-function is a common mechanism associated with missense KCNQ2 variants. Importantly, we observed genotype-dependent differences in the response of KCNQ2 variants to retigabine, a proposed precision therapy for KCNQ2 developmental and epileptic encephalopathy.
Published: 2022
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3. Whole‐exome and HLA sequencing in Febrile infection‐related epilepsy syndrome

Author: Ingo Helbig, Giulia Barcia, Manuela Pendziwiat, Shiva Ganesan, Stefanie H. Mueller, Katherine L. Helbig, Priya Vaidiswaran, Julie Xian, Peter D. Galer, Zaid Afawi, Nicola Specchio, Gerhard Kluger, Gregor Kuhlenbäumer, Silke Appenzeller, Michael Wittig, Uri Kramer, Andreas vanBaalen, Rima Nabbout, and FIRES Genetics Study Group
Subjects: Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571, Neurology. Diseases of the nervous system, RC346-429
Abstract: Abstract Febrile infection‐related epilepsy syndrome (FIRES) is a devastating epilepsy characterized by new‐onset refractory status epilepticus with a prior febrile infection. We performed exome sequencing in 50 individuals with FIRES, including 27 patient–parent trios and 23 single probands, none of whom had pathogenic variants in established genes for epilepsies or neurodevelopmental disorders. We also performed HLA sequencing in 29 individuals with FIRES and 529 controls, which failed to identify prominent HLA alleles. The genetic architecture of FIRES is substantially different from other developmental and epileptic encephalopathies, and the underlying etiology remains elusive, requiring novel approaches to identify the underlying causative factors.
Published: 2020
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4. Gene family information facilitates variant interpretation and identification of disease-associated genes in neurodevelopmental disorders

Author: Dennis Lal, Patrick May, Eduardo Perez-Palma, Kaitlin E. Samocha, Jack A. Kosmicki, Elise B. Robinson, Rikke S. Møller, Roland Krause, Peter Nürnberg, Sarah Weckhuysen, Peter De Jonghe, Renzo Guerrini, Lisa M. Niestroj, Juliana Du, Carla Marini, EuroEPINOMICS-RES Consortium, James S. Ware, Mitja Kurki, Padhraig Gormley, Sha Tang, Sitao Wu, Saskia Biskup, Annapurna Poduri, Bernd A. Neubauer, Bobby P. C. Koeleman, Katherine L. Helbig, Yvonne G. Weber, Ingo Helbig, Amit R. Majithia, Aarno Palotie, and Mark J. Daly
Subjects: Paralogs, Gene family, Conservation, Missense variants, Neurodevelopmental disorders, Medicine, Genetics, QH426-470
Abstract: Abstract Background Classifying pathogenicity of missense variants represents a major challenge in clinical practice during the diagnoses of rare and genetic heterogeneous neurodevelopmental disorders (NDDs). While orthologous gene conservation is commonly employed in variant annotation, approximately 80% of known disease-associated genes belong to gene families. The use of gene family information for disease gene discovery and variant interpretation has not yet been investigated on a genome-wide scale. We empirically evaluate whether paralog-conserved or non-conserved sites in human gene families are important in NDDs. Methods Gene family information was collected from Ensembl. Paralog-conserved sites were defined based on paralog sequence alignments; 10,068 NDD patients and 2078 controls were statistically evaluated for de novo variant burden in gene families. Results We demonstrate that disease-associated missense variants are enriched at paralog-conserved sites across all disease groups and inheritance models tested. We developed a gene family de novo enrichment framework that identified 43 exome-wide enriched gene families including 98 de novo variant carrying genes in NDD patients of which 28 represent novel candidate genes for NDD which are brain expressed and under evolutionary constraint. Conclusion This study represents the first method to incorporate gene family information into a statistical framework to interpret variant data for NDDs and to discover new NDD-associated genes.
Published: 2020
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5. Biallelic VARS variants cause developmental encephalopathy with microcephaly that is recapitulated in vars knockout zebrafish

Author: Aleksandra Siekierska, Hannah Stamberger, Tine Deconinck, Stephanie N. Oprescu, Michèle Partoens, Yifan Zhang, Jo Sourbron, Elias Adriaenssens, Patrick Mullen, Patrick Wiencek, Katia Hardies, Jeong-Soo Lee, Hoi-Khoanh Giong, Felix Distelmaier, Orly Elpeleg, Katherine L. Helbig, Joseph Hersh, Sedat Isikay, Elizabeth Jordan, Ender Karaca, Angela Kecskes, James R. Lupski, Reka Kovacs-Nagy, Patrick May, Vinodh Narayanan, Manuela Pendziwiat, Keri Ramsey, Sampathkumar Rangasamy, Deepali N. Shinde, Ronen Spiegel, Vincent Timmerman, Sarah von Spiczak, Ingo Helbig, C4RCD Research Group, AR working group of the EuroEPINOMICS RES Consortium, Sarah Weckhuysen, Christopher Francklyn, Anthony Antonellis, Peter de Witte, and Peter De Jonghe
Subjects: Science
Abstract: tRNAs are linked with their cognate amino acid by aminoacyl tRNA synthetases (ARS). Here, the authors report a developmental encephalopathy associated with biallelic VARS variants (valyl-tRNA synthetase) that lead to loss of function, as determined by several in vitro assays and a vars knockout zebrafish model.
Published: 2019
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6. Genotype-phenotype correlations in SCN8A-related disorders reveal prognostic and therapeutic implications

Author: Roseline Caume, M Scott Perry, Massimo Mastrangelo, Margarete Koch-Hogrebe, Pasquale Striano, Karen Müller-Schlüter, Petra Laššuthová, Monisa D. Wagner, Ingo Helbig, Stephan Lauxmann, Emmanuel Scalais, Marie-Cécile Nassogne, Silvia Masnada, Henrike O. Heyne, Konrad Platzer, Frederic Bilan, Chloe A Stutterd, Sonja Walsh, Katrine M Johannesen, Damien Lederer, Ngoc Minh Le, Christina Fenger, Daniel Tibussek, Lukas Sonnenberg, Andrea Berger, Yuanyuan Liu, Mikhail Abramov, Karen E. Wain, Sergey Korostelev, P Y Billie Au, Elena L. Dadali, An-Sofie Schoonjans, Cornelia Betzler, Artem Borovikov, Johanna Krüger, Maert Rannap, Sebastian Lebon, Nils A Koch, Nancy Eisenhauer, Judith Kroell-Seger, Julian Schubert, Marije Meuwissen, Caroline Lund, Mark Fitzgerald, Federico Zara, Siddharth Srivastava, Claudia M Bonardi, Pia Zacher, Haim Bassan, Arve Vøllo, Katherine B. Howell, Francesca Darra, Guido Rubboli, Stephen W. Scherer, Bénédicte Gérard, Stefano Sartori, Annapurna Poduri, Helene Verhelst, Katalin Sterbova, Mathilde Nizon, Marketa Vlckova, Christina E. Hoei-Hansen, Renzo Guerrini, Ilya V. Kanivets, Juliann M. Savatt, Johannes Rebstock, Jakob Christensen, Cecilia Altuzarra, Dennis Lal, Judith S. Verhoeven, Agathe Roubertie, Constanze Heine, Dagmar Wieczorek, Ingo Borggraefe, Aster V. E. Harder, Anne Destrée, Wen-Hann Tan, Tobias Brünger, Shoji Ichikawa, Laura Canafoglia, Mahmoud Koko, Sergey Kutsev, Sabine Grønborg, Patrizia Accorsi, Heather E. Olson, Bert van der Zwaag, Cathrine E Gjerulfsen, Patrick May, A. A. Sharkov, M. Mahdi Motazacker, Manuela Pendziwiat, Richard J. Leventer, Anna Jansen, Lucio Giordano, Holger Lerche, Carla Marini, Karl Martin Klein, Eva H. Brilstra, Ahmed Eltokhi, Ethan M. Goldberg, Walid Fazeli, Rikke S. Møller, Dorota Hoffman-Zacharska, Michael Alber, Susanne Ruf, Jennifer L. Howe, Phillis Lakeman, Josua Kegele, Katherine L. Helbig, Marga Buzatu, Alice W Ho, Jan Benda, Ilona Krey, Marion Gérard, Sara Matricardi, Thomas U. Mayer, Philippe Gelisse, Jong M. Rho, Johannes R. Lemke, Pierangelo Veggiotti, Tobias Loddenkemper, Gaetan Lesca, Ulrike B. S. Hedrich, Silvana Franceschetti, Elena Gardella, Irina Mishina, María Vaccarezza, Timo Roser, Public Health Sciences, Mental Health and Wellbeing research group, Neurogenetics, Neuroprotection & Neuromodulation, Pediatrics, Human Genetics, ANS - Complex Trait Genetics, ARD - Amsterdam Reproduction and Development, Human genetics, and Amsterdam Reproduction & Development (AR&D)
Subjects: medicine.medical_specialty, SCN8A, Gastroenterology, Epilepsy, Sodium channel blocker, Neurodevelopmental disorder, Seizures, Intellectual Disability, Internal medicine, medicine, Humans, Missense mutation, genetics, Generalized epilepsy, Genetic Association Studies, Benign familial infantile epilepsy, Generalized, business.industry, Infant, personalized medicine, Prognosis, medicine.disease, Phenotype, Settore MED/39 - Neuropsichiatria Infantile, NAV1.6 Voltage-Gated Sodium Channel, Mutation, epilepsy, Original Article, Epilepsy, Generalized, Human medicine, Neurology (clinical), Age of onset, business, Epileptic Syndromes, Sodium Channel Blockers
Abstract: We report detailed functional analyses and genotype-phenotype correlations in 392 individuals carrying disease-causing variants in SCN8A, encoding the voltage-gated Na+ channel Nav1.6, with the aim of describing clinical phenotypes related to functional effects. Six different clinical subgroups were identified: Group 1, benign familial infantile epilepsy (n = 15, normal cognition, treatable seizures); Group 2, intermediate epilepsy (n = 33, mild intellectual disability, partially pharmaco-responsive); Group 3, developmental and epileptic encephalopathy (n = 177, severe intellectual disability, majority pharmaco-resistant); Group 4, generalized epilepsy (n = 20, mild to moderate intellectual disability, frequently with absence seizures); Group 5, unclassifiable epilepsy (n = 127); and Group 6, neurodevelopmental disorder without epilepsy (n = 20, mild to moderate intellectual disability). Those in Groups 1–3 presented with focal or multifocal seizures (median age of onset: 4 months) and focal epileptiform discharges, whereas the onset of seizures in patients with generalized epilepsy was later (median: 42 months) with generalized epileptiform discharges. We performed functional studies expressing missense variants in ND7/23 neuroblastoma cells and primary neuronal cultures using recombinant tetrodotoxin-insensitive human Nav1.6 channels and whole-cell patch-clamping. Two variants causing developmental and epileptic encephalopathy showed a strong gain-of-function (hyperpolarizing shift of steady-state activation, strongly increased neuronal firing rate) and one variant causing benign familial infantile epilepsy or intermediate epilepsy showed a mild gain-of-function (defective fast inactivation, less increased firing). In contrast, all three variants causing generalized epilepsy induced a loss-of-function (reduced current amplitudes, depolarizing shift of steady-state activation, reduced neuronal firing). Functional effects were known for 170 individuals. All 136 individuals carrying a functionally tested gain-of-function variant had either focal (n = 97, Groups 1–3) or unclassifiable (n = 39) epilepsy, whereas 34 individuals with a loss-of-function variant had either generalized (n = 14), no (n = 11) or unclassifiable (n = 6) epilepsy; only three had developmental and epileptic encephalopathy. Computational modelling in the gain-of-function group revealed a significant correlation between the severity of the electrophysiological and clinical phenotypes. Gain-of-function variant carriers responded significantly better to sodium channel blockers than to other anti-seizure medications, and the same applied for all individuals in Groups 1–3. In conclusion, our data reveal clear genotype-phenotype correlations between age at seizure onset, type of epilepsy and gain- or loss-of-function effects of SCN8A variants. Generalized epilepsy with absence seizures is the main epilepsy phenotype of loss-of-function variant carriers and the extent of the electrophysiological dysfunction of the gain-of-function variants is a main determinant of the severity of the clinical phenotype in focal epilepsies. Our pharmacological data indicate that sodium channel blockers present a treatment option in SCN8A-related focal epilepsy with onset in the first year of life.
Published: 2022
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7. Human

Author: Aguan D, Wei, Paul, Wakenight, Theresa A, Zwingman, Angela M, Bard, Nikhil, Sahai, Marjolein H, Willemsen, Helenius J, Schelhaas, Alexander P A, Stegmann, Judith S, Verhoeven, Stella A, de Man, Marja W, Wessels, Tjitske, Kleefstra, Deepali N, Shinde, Katherine L, Helbig, Alice, Basinger, Victoria F, Wagner, David, Rodriguez-Buritica, Emily, Bryant, John J, Millichap, Kathleen J, Millen, William B, Dobyns, Jan-Marino, Ramirez, and Franck K, Kalume
Subjects: Mice, Cricetulus, Epilepsy, HEK293 Cells, KCNQ Potassium Channels, Seizures, Cricetinae, Intellectual Disability, Mutation, Missense, Animals, Humans, Child, Research Article
Abstract: We identified six novel de novo human KCNQ5 variants in children with motor/language delay, intellectual disability (ID), and/or epilepsy by whole exome sequencing. These variants, comprising two nonsense and four missense alterations, were functionally characterized by electrophysiology in HEK293/CHO cells, together with four previously reported KCNQ5 missense variants (Lehman A, Thouta S, Mancini GM, Naidu S, van Slegtenhorst M, McWalter K, Person R, Mwenifumbo J, Salvarinova R; CAUSES Study; EPGEN Study; Guella I, McKenzie MB, Datta A, Connolly MB, Kalkhoran SM, Poburko D, Friedman JM, Farrer MJ, Demos M, Desai S, Claydon T. Am J Hum Genet 101: 65–74, 2017). Surprisingly, all eight missense variants resulted in gain of function (GOF) due to hyperpolarized voltage dependence of activation or slowed deactivation kinetics, whereas the two nonsense variants were confirmed to be loss of function (LOF). One severe GOF allele (P369T) was tested and found to extend a dominant GOF effect to heteromeric KCNQ5/3 channels. Clinical presentations were associated with altered KCNQ5 channel gating: milder presentations with LOF or smaller GOF shifts in voltage dependence [change in voltage at half-maximal conduction (ΔV(50)) = ∼−15 mV] and severe presentations with larger GOF shifts in voltage dependence (ΔV(50) = ∼−30 mV). To examine LOF pathogenicity, two Kcnq5 LOF mouse lines were created with CRISPR/Cas9. Both lines exhibited handling- and thermal-induced seizures and abnormal cortical EEGs consistent with epileptiform activity. Our study thus provides evidence for in vivo KCNQ5 LOF pathogenicity and strengthens the contribution of both LOF and GOF mutations to global pediatric neurological impairment, including ID/epilepsy. NEW & NOTEWORTHY Six novel de novo human KCNQ5 variants were identified from children with neurodevelopmental delay, intellectual disability, and/or epilepsy. Expression of these variants along with four previously reported KCNQ5 variants from a similar cohort revealed GOF potassium channels, negatively shifted in V(50) of activation and/or delayed deactivation kinetics. GOF is extended to KCNQ5/3 heteromeric channels, making these the predominant channels affected in heterozygous de novo patients. Kcnq5 LOF mice exhibited seizures, consistent with in vivo pathogenicity.
Published: 2023

8. Human KCNQ5 de novo Mutations Underlie Epilepsy and Intellectual Disability

Author: Aguan D. Wei, Paul Wakenight, Theresa A. Zwingman, Angela M. Bard, Nikhil Sahai, Marjolein H. Willemsen, Helenius J. Schelhaas, Alexander P. A. Stegmann, Judith S. Verhoeven, Stella A. de Man, Marja W. Wessels, Tjitske Kleefstra, Deepali N. Shinde, Katherine L. Helbig, Alice Basinger, Victoria F. Wagner, David Rodriguez-Buritica, Emily Bryant, John J. Millichap, Kathleen J. Millen, William B. Dobyns, Jan-Marino Ramirez, Franck K. Kalume, Clinical Genetics, MUMC+: DA KG Polikliniek (9), MUMC+: DA KG Lab Centraal Lab (9), and RS: FHML non-thematic output
Subjects: POTASSIUM CHANNEL GENE, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Physiology, General Neuroscience, FUNCTIONAL EXPRESSION, M current, MOUSE MODEL, All institutes and research themes of the Radboud University Medical Center, channelopathy, VOLTAGE SENSOR, intellectual disability, SIGNALING COMPLEX, OF-FUNCTION MUTATIONS, SUBUNIT, epilepsy, SEIZURES, NEURONAL EXCITABILITY, DRAVET SYNDROME, KCNQ5
Abstract: We identified six novel de novo human KCNQ5 variants in children with motor/language delay, intellectual disability (ID), and/or epilepsy by whole exome sequencing. These variants, comprising two nonsense and four missense alterations, were functionally characterized by electrophysiology in HEK293/CHO cells, together with four previously reported KCNQ5 missense variants (Lehman A, Thouta S, Mancini GM, Naidu S, van Slegtenhorst M, McWalter K, Person R, Mwenifumbo J, Salvarinova R; CAUSES Study; EPGEN Study; Guella I, McKenzie MB, Datta A, Connolly MB, Kalkhoran SM, Poburko D, Friedman JM, Farrer MJ, Demos M, Desai S, Claydon T. Am J Hum Genet 101: 65-74, 2017). Surprisingly, all eight missense variants resulted in gain of function (GOF) due to hyperpolarized voltage dependence of activation or slowed deactivation kinetics, whereas the two nonsense variants were confirmed to be loss of function (LOF). One severe GOF allele (P369T) was tested and found to extend a dominant GOF effect to heteromeric KCNQ5/3 channels. Clinical presentations were associated with altered KCNQ5 channel gating: milder presentations with LOF or smaller GOF shifts in voltage dependence [change in voltage at half-maximal conduction (ΔV50) = ~-15 mV] and severe presentations with larger GOF shifts in voltage dependence (ΔV50 = ~30 mV). To examine LOF pathogenicity, two Kcnq5 LOF mouse lines were created with CRISPR/Cas9. Both lines exhibited handling- and thermal-induced seizures and abnormal cortical EEGs consistent with epileptiform activity. Our study thus provides evidence for in vivo KCNQ5 LOF pathogenicity and strengthens the contribution of both LOF and GOF mutations to global pediatric neurological impairment, including ID/epilepsy.
Published: 2022
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9. Computational analysis of 10,860 phenotypic annotations in individuals with SCN2A-related disorders

Author: Margaret O'Brien, Shridhar Parthasarathy, Eryn Fitch, Ingo Helbig, Roland Krause, Shiva Ganesan, Veronica Codoni, Katherine Crawford, Deanne Taylor, Colin A Ellis, Julie Xian, Peter D. Galer, David Lewis-Smith, Katherine L. Helbig, Michael C. Kaufman, and Laura Conway
Subjects: NAV1.2 Voltage-Gated Sodium Channel, Infant, Newborn, Neonatal onset, Computational biology, Biology, medicine.disease, Phenotype, Article, Epileptic spasms, Seizures, Human Phenotype Ontology, medicine, Humans, Missense mutation, Autism, Computational analysis, Spasms, Infantile, Genetic Association Studies, Genetics (clinical)
Abstract: Purpose Pathogenic variants in SCN2A cause a wide range of neurodevelopmental phenotypes. Reports of genotype–phenotype correlations are often anecdotal, and the available phenotypic data have not been systematically analyzed. Methods We extracted phenotypic information from primary descriptions of SCN2A-related disorders in the literature between 2001 and 2019, which we coded in Human Phenotype Ontology (HPO) terms. With higher-level phenotype terms inferred by the HPO structure, we assessed the frequencies of clinical features and investigated the association of these features with variant classes and locations within the NaV1.2 protein. Results We identified 413 unrelated individuals and derived a total of 10,860 HPO terms with 562 unique terms. Protein-truncating variants were associated with autism and behavioral abnormalities. Missense variants were associated with neonatal onset, epileptic spasms, and seizures, regardless of type. Phenotypic similarity was identified in 8/62 recurrent SCN2A variants. Three independent principal components accounted for 33% of the phenotypic variance, allowing for separation of gain-of-function versus loss-of-function variants with good performance. Conclusion Our work shows that translating clinical features into a computable format using a standardized language allows for quantitative phenotype analysis, mapping the phenotypic landscape of SCN2A-related disorders in unprecedented detail and revealing genotype–phenotype correlations along a multidimensional spectrum.
Published: 2021
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10. Variants in the SK2 channel gene (KCNN2) lead to dominant neurodevelopmental movement disorders

Author: Sylvia A. Huisman, Fanny Mochel, Christel Depienne, Roberto Canitano, Sara S. Cathey, Kimberly Nugent, Konrad Platzer, Katherine L. Helbig, Deepali N. Shinde, Diego Lopergolo, Sandra Yang, Francesca Mari, Astrid S. Plomp, Berten Ceulemans, Sarah Weckhuysen, Agnès Rastetter, Nadja Ehmke, Julien Thevenon, Rami Abou Jamra, Elisa Benetti, Daniela del Gaudio, Elizabeth Roeder, Darrel Waggoner, Raymond J. Louie, Shawn Kacker, Manuel Holtgrewe, Alessandra Renieri, Susanne B. Kamphausen, Denise Horn, Ange Line Bruel, Carine Dalle, Quinten Waisfisz, Frank J. Kaiser, Golder N. Wilson, Human genetics, Pediatric surgery, Amsterdam Reproduction & Development (AR&D), Human Genetics, and Paediatric Genetics
Subjects: Male, 0301 basic medicine, Patch-Clamp Techniques, Movement disorders, Small-Conductance Calcium-Activated Potassium Channels, Medizin, Haploinsufficiency, 0302 clinical medicine, Missense mutation, Exome, Child, Frameshift Mutation, Exome sequencing, Genetics, Movement Disorders, Learning Disabilities, Middle Aged, Magnetic Resonance Imaging, White Matter, developmental delay, Child, Preschool, medicine.symptom, SK2 channel, KCNN2, ataxia, tremor, Adolescent, Adult, Cerebellar Ataxia, Electrophysiological Phenomena, Genetic Variation, Humans, Intellectual Disability, Mutation, Missense, Neurodevelopmental Disorders, Young Adult, Ataxia, Biology, Frameshift mutation, 03 medical and health sciences, medicine, Preschool, Cerebellar ataxia, 030104 developmental biology, Mutation, Neurology (clinical), Missense, 030217 neurology & neurosurgery
Abstract: KCNN2 encodes the small conductance calcium-activated potassium channel 2 (SK2). Rodent models with spontaneous Kcnn2 mutations show abnormal gait and locomotor activity, tremor and memory deficits, but human disorders related to KCNN2 variants are largely unknown. Using exome sequencing, we identified a de novo KCNN2 frameshift deletion in a patient with learning disabilities, cerebellar ataxia and white matter abnormalities on brain MRI. This discovery prompted us to collect data from nine additional patients with de novo KCNN2 variants (one nonsense, one splice site, six missense variants and one in-frame deletion) and one family with a missense variant inherited from the affected mother. We investigated the functional impact of six selected variants on SK2 channel function using the patch-clamp technique. All variants tested but one, which was reclassified to uncertain significance, led to a loss-of-function of SK2 channels. Patients with KCNN2 variants had motor and language developmental delay, intellectual disability often associated with early-onset movement disorders comprising cerebellar ataxia and/or extrapyramidal symptoms. Altogether, our findings provide evidence that heterozygous variants, likely causing a haploinsufficiency of the KCNN2 gene, lead to novel autosomal dominant neurodevelopmental movement disorders mirroring phenotypes previously described in rodents.
Published: 2020
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11. Semantic Similarity Analysis Reveals Robust Gene-Disease Relationships in Developmental and Epileptic Encephalopathies

Author: Rhys H. Thomas, Ingo Helbig, David Lewis-Smith, Hiltrud Muhle, Lacey Smith, Colin A Ellis, Manuela Pendziwiat, Epgp Investigators, Annika Rademacher, Annapurna Poduri, Simone Seiffert, Andreas van Baalen, Sarah E McKeown, Roland Krause, Shiva Ganesan, Sarah von Spiczak, Katherine L. Helbig, Peter D. Galer, and Yvonne G. Weber
Subjects: Male, 0301 basic medicine, GABA Plasma Membrane Transport Proteins, Gene Expression, Human Phenotype Ontology, Biology, computational phenotypes, Article, Speech Disorders, EEG with generalized slow activity, Cohort Studies, 03 medical and health sciences, Munc18 Proteins, Shab Potassium Channels, 0302 clinical medicine, Semantic similarity, Similarity (network science), Seizures, Terminology as Topic, Exome Sequencing, electronic medical records, Genetics, Humans, STXBP1, whole-exome sequencing, neurogenetic disorders, Gene, Genetics (clinical), Exome sequencing, Phenotype, Semantics, NAV1.1 Voltage-Gated Sodium Channel, childhood epilepsies, developmental and epileptic encephalopathies, Gene Ontology, 030104 developmental biology, Child, Preschool, Mutation, Female, Genetics & genetic processes [F10] [Life sciences], Génétique & processus génétiques [F10] [Sciences du vivant], Spasms, Infantile, 030217 neurology & neurosurgery
Abstract: Summary More than 100 genetic etiologies have been identified in developmental and epileptic encephalopathies (DEEs), but correlating genetic findings with clinical features at scale has remained a hurdle because of a lack of frameworks for analyzing heterogenous clinical data. Here, we analyzed 31,742 Human Phenotype Ontology (HPO) terms in 846 individuals with existing whole-exome trio data and assessed associated clinical features and phenotypic relatedness by using HPO-based semantic similarity analysis for individuals with de novo variants in the same gene. Gene-specific phenotypic signatures included associations of SCN1A with “complex febrile seizures” (HP: 0011172; p = 2.1 × 10−5) and “focal clonic seizures” (HP: 0002266; p = 8.9 × 10−6), STXBP1 with “absent speech” (HP: 0001344; p = 1.3 × 10−11), and SLC6A1 with “EEG with generalized slow activity” (HP: 0010845; p = 0.018). Of 41 genes with de novo variants in two or more individuals, 11 genes showed significant phenotypic similarity, including SCN1A (n = 16, p < 0.0001), STXBP1 (n = 14, p = 0.0021), and KCNB1 (n = 6, p = 0.011). Including genetic and phenotypic data of control subjects increased phenotypic similarity for all genetic etiologies, whereas the probability of observing de novo variants decreased, emphasizing the conceptual differences between semantic similarity analysis and approaches based on the expected number of de novo events. We demonstrate that HPO-based phenotype analysis captures unique profiles for distinct genetic etiologies, reflecting the breadth of the phenotypic spectrum in genetic epilepsies. Semantic similarity can be used to generate statistical evidence for disease causation analogous to the traditional approach of primarily defining disease entities through similar clinical features.
Published: 2020
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12. A longitudinal footprint of genetic epilepsies using automated electronic medical record interpretation

Author: Shiva Ganesan, Peter D. Galer, Katherine L. Helbig, Sarah E. McKeown, Margaret O’Brien, Alexander K. Gonzalez, Alex S. Felmeister, Pouya Khankhanian, Colin A. Ellis, and Ingo Helbig
Subjects: 0301 basic medicine, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, childhood epilepsy, electronic medical records, Human Phenotype Ontology, neurogenetics, 030217 neurology & neurosurgery, Genetics (clinical), Article
Abstract: Purpose Childhood epilepsies have a strong genetic contribution, but the disease trajectory for many genetic etiologies remains unknown. Electronic medical record (EMR) data potentially allow for the analysis of longitudinal clinical information but this has not yet been explored. Methods We analyzed provider-entered neurological diagnoses made at 62,104 patient encounters from 658 individuals with known or presumed genetic epilepsies. To harmonize clinical terminology, we mapped clinical descriptors to Human Phenotype Ontology (HPO) terms and inferred higher-level phenotypic concepts. We then binned the resulting 286,085 HPO terms to 100 3-month time intervals and assessed gene–phenotype associations at each interval. Results We analyzed a median follow-up of 6.9 years per patient and a cumulative 3251 patient years. Correcting for multiple testing, we identified significant associations between “Status epilepticus” with SCN1A at 1.0 years, “Severe intellectual disability” with PURA at 9.75 years, and “Infantile spasms” and “Epileptic spasms” with STXBP1 at 0.5 years. The identified associations reflect known clinical features of these conditions, and manual chart review excluded provider bias. Conclusion Some aspects of the longitudinal disease histories can be reconstructed through EMR data and reveal significant gene–phenotype associations, even within closely related conditions. Gene-specific EMR footprints may enable outcome studies and clinical decision support.
Published: 2020

13. Whole‐exome and HLA sequencing in Febrile infection‐related epilepsy syndrome

Author: Rima Nabbout, Nicola Specchio, Ingo Helbig, Giulia Barcia, Michael Wittig, Peter D. Galer, Stefanie H. Mueller, Uri Kramer, Manuela Pendziwiat, Andreas van Baalen, Gregor Kuhlenbäumer, Silke Appenzeller, Zaid Afawi, Katherine L. Helbig, Shiva Ganesan, Gerhard Kluger, Priya Vaidiswaran, Julie Xian, and Psychiatry
Subjects: Male, 0301 basic medicine, Proband, Drug Resistant Epilepsy, Adolescent, Fever, Neurosciences. Biological psychiatry. Neuropsychiatry, Status epilepticus, Human leukocyte antigen, Brief Communication, Communicable Diseases, 03 medical and health sciences, Epilepsy, Status Epilepticus, 0302 clinical medicine, HLA Antigens, Exome Sequencing, medicine, Humans, RC346-429, Child, Exome, Exome sequencing, business.industry, General Neuroscience, Sequence Analysis, DNA, medicine.disease, Febrile infection related epilepsy syndrome, 030104 developmental biology, nervous system, Child, Preschool, Epilepsy syndromes, Immunology, Female, Neurology. Diseases of the nervous system, Neurology (clinical), medicine.symptom, business, Epileptic Syndromes, 030217 neurology & neurosurgery, RC321-571
Abstract: Febrile infection‐related epilepsy syndrome (FIRES) is a devastating epilepsy characterized by new‐onset refractory status epilepticus with a prior febrile infection. We performed exome sequencing in 50 individuals with FIRES, including 27 patient–parent trios and 23 single probands, none of whom had pathogenic variants in established genes for epilepsies or neurodevelopmental disorders. We also performed HLA sequencing in 29 individuals with FIRES and 529 controls, which failed to identify prominent HLA alleles. The genetic architecture of FIRES is substantially different from other developmental and epileptic encephalopathies, and the underlying etiology remains elusive, requiring novel approaches to identify the underlying causative factors.
Published: 2020
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14. Caregiver assessment of quality of life in individuals with genetic developmental and epileptic encephalopathies

Author: Stacey R. Cohen, Ingo Helbig, Michael C. Kaufman, Leah Schust Myers, Laura Conway, and Katherine L. Helbig
Subjects: Developmental Neuroscience, Caregivers, Autism Spectrum Disorder, Cerebral Palsy, Surveys and Questionnaires, Pediatrics, Perinatology and Child Health, Quality of Life, Humans, Neurology (clinical)
Abstract: To summarize quality of life (QoL) and its determinants, including disease severity, in individuals with developmental and epileptic encephalopathies (DEEs) through a tailored questionnaire.A questionnaire containing 89 items addressing demographic characteristics, genetic diagnosis, clinical features, and QoL was distributed to primary caregivers of individuals with DEEs through patient advocacy organizations. Composite scores were generated from the mean values of QoL items, grouped into domain scores.Out of 176 received responses, the most common genetic diagnoses reported were SCN2A (n=42/173, 24%), SLC6A1 (n=28/173, 16%), SCN1A (n=22/173, 13%), and KCNQ2 (n=21/173, 12%). Composite QoL scores centered around a mean score of 61.67 of 100 (SD 17.10). QoL scores were strongly associated with the number of days minimally disrupted by seizures, medication side effects, genetic diagnosis, and community type. The mean QoL scores for individuals with DEEs was significantly lower than for individuals with Rett syndrome, cerebral palsy, autism spectrum disorder, and Down syndrome.QoL in DEEs can be assessed through a standardized instrument. QoL only partially overlaps with objective measurements of disease severity and may represent an independent outcome measure in precision medicine trials.
Published: 2022

15. A Recurrent Missense Variant in AP2M1 Impairs Clathrin-Mediated Endocytosis and Causes Developmental and Epileptic Encephalopathy

Author: Batsal Devkota, José M. Serratosa, Joel N. Hirschhorn, Renzo Guerrini, Patrick May, Johanna A. Jähn, Paul Avillach, Yvonne G. Weber, Sha Tang, Kaja Kristine Selmer, Joseph J. Shen, Annika Rademacher, Joseph Peeden, Ulrich Stephani, Judson Kilbourn, Niklas Schwarz, Deb K. Pal, Lacey Smith, Trine Bjørg Hammer, Carla Marini, Deanne Taylor, Ingo Helbig, Rudi Balling, Arvid Suls, Holger Lerche, Karl Martin Klein, Simone Seiffert, Annapurna Poduri, Bobby P. C. Koeleman, Tania López-Hernández, Deepali N. Shinde, Stéphanie Baulac, Sawona Biswas, Eric LeGuern, Peter D. Galer, Volker Haucke, Katherine L. Helbig, Ian D. Krantz, Aarno Palotie, Sarah Weckhuysen, Nadja Hümpfer, Tiina Talvik, Rikke S. Møller, Roland Krause, Allison Heath, Dorota Hoffman-Zacharska, Nina Barišić, Peter De Jonghe, Hiltrud Muhle, In-Hee Lee, Kenneth D. Mandl, Felix Benninger, Dana Craiu, Florence T. Bourgeois, Colin A Ellis, Sanjay M. Sisodiya, Christel Depienne, Barbara Hallinan, Eric D. Marsh, Susanne Schubert-Bast, Manuela Pendziwiat, Kristen L. Sund, Federico Zara, Tracy A. Glauser, Katalin Štěrbová, Johannes R. Lemke, Oded Shor, Anna-Elina Lehesjoki, Helle Hjalgrim, Anna Bartels, Vladimir Komarek, Peter White, Tarja Linnankivi, Hande Caglayan, Sarah von Spiczak, Shiva Ganesan, Felix Rosenow, Sek Won Kong, Pasquale Striano, EuroEPINOMICS-RES Consortium, GRIN Consortium, Department of Medical and Clinical Genetics, Centre of Excellence in Complex Disease Genetics, Aarno Palotie / Principal Investigator, Genomics of Neurological and Neuropsychiatric Disorders, Institute for Molecular Medicine Finland, HUS Children and Adolescents, and Children's Hospital
Subjects: 0301 basic medicine, PROTEIN, ILAE COMMISSION, clathrin-mediated endocytosis, 3124 Neurology and psychiatry, Mice, Epilepsy, 0302 clinical medicine, BINDING, Conditional gene knockout, Missense mutation, Child, Genetics (clinical), Mice, Knockout, Genetics, Brain Diseases, neurodevelopmental disorders, Phenotype, Endocytosis, Adaptor Protein Complex mu Subunits, Child, Preschool, Female, POSITION PAPER, RECRUITMENT, Adolescent, computational phenotypes, developmental and epileptic encephalopathy, Human Phenotype Ontology, synaptic transmission, Adaptor Protein Complex 2, Mutation, Missense, Biology, CLASSIFICATION, Article, 03 medical and health sciences, Exome Sequencing, medicine, Animals, Humans, Synaptic vesicle recycling, ADAPTER AP-2, Generalized epilepsy, 3112 Neurosciences, Infant, Receptor-mediated endocytosis, medicine.disease, Clathrin, 030104 developmental biology, DE-NOVO MUTATIONS, 3111 Biomedicine, Human medicine, 030217 neurology & neurosurgery
Abstract: The developmental and epileptic encephalopathies (DEEs) are heterogeneous disorders with a strong genetic contribution, but the underlying genetic etiology remains unknown in a significant proportion of individuals. To explore whether statistical support for genetic etiologies can be generated on the basis of phenotypic features, we analyzed whole-exome sequencing data and phenotypic similarities by using Human Phenotype Ontology (HPO) in 314 individuals with DEEs. We identified a de novo c.508C>T (p.Arg170Trp) variant in AP2M1 in two individuals with a phenotypic similarity that was higher than expected by chance (p = 0.003) and a phenotype related to epilepsy with myoclonic-atonic seizures. We subsequently found the same de novo variant in two individuals with neurodevelopmental disorders and generalized epilepsy in a cohort of 2,310 individuals who underwent diagnostic whole-exome sequencing. AP2M1 encodes the mu-subunit of the adaptor protein complex 2 (AP-2), which is involved in clathrin-mediated endocytosis (CME) and synaptic vesicle recycling. Modeling of protein dynamics indicated that the p.Arg170Trp variant impairs the conformational activation and thermodynamic entropy of the AP-2 complex. Functional complementation of both the mu-subunit carrying the p.Arg170Trp variant in human cells and astrocytes derived from AP-2 mu conditional knockout mice revealed a significant impairment of CME of transferrin. In contrast, stability, expression levels, membrane recruitment, and localization were not impaired, suggesting a functional alteration of the AP-2 complex as the underlying disease mechanism. We establish a recurrent pathogenic variant in AP2M1 as a cause of DEEs with distinct phenotypic features, and we implicate dysfunction of the early steps of endocytosis as a disease mechanism in epilepsy.
Published: 2019
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16. 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

17. Genotype-phenotype correlations in SCN8A-related disorders reveal prognostic and therapeutic implications

Author: Arve Vøllo, Stephen W. Scherer, Elena Gardella, Irina Mishina, María Vaccarezza, Jennifer L. Howe, Sebastian Lebon, Josua Kegele, Gaetan Lesca, Timo Roser, Silvia Masnada, Johannes Rebstock, Marga Buzatu, Damien Lederer, Ingo Borggraefe, Tobias Brünger, Ulrike B. S. Hedrich, Sergey Korostelev, Frédéric Bilan, Ahmed Eltokhi, M. Mahdi Motazacker, Karen E. Wain, Susanne Ruf, Manuela Pendziwiat, Lukas Sonnenberg, Yuanyuan Liu, Alice W Ho, Silvana Franceschetti, Jan Benda, Ethan M. Goldberg, Helene Verhelst, Julian Schubert, Juliann M. Savatt, Mathilde Nizon, Caroline Lund, Katherine B. Howell, Tobias Loddenkemper, Katherine L. Helbig, Cornelia Betzler, Roseline Caume, Francesca Darra, Richard J. Leventer, Christina Fenger, Pierangelo Veggiotti, Ilona Krey, Nancy Eisenhauer, Andrea Berger, Pasquale Striano, Heather E. Olson, An-Sofie Schoonjans, M Scott Perry, Stephan Lauxmann, Emmanuel Scalais, Petra Laššuthová, Monisa D. Wagner, Ilya V. Kanivets, A. A. Sharkov, P Y Billie Au, Mahmoud Koko, Siddharth Srivastava, Jakob Christensen, Artem Borovikov, Mette U Schmidt-Petersen, Anna Jansen, Judith S. Verhoeven, Johanna Krüger, Claudia M Bonardi, Shoji Ichikawa, Patrick May, Sabine Grønborg, Johannes R. Lemke, Marije Meuwissen, Katalin Sterbova, Mark Fitzgerald, Lucio Giordano, Holger Lerche, Mikhail Abramov, Bénédicte Gérard, Elena L. Dadali, Cecilia Altuzarra, Aster V. E. Harder, Stefano Sartori, Katrine M Johannesen, Sergey Kutsev, Maert Rannap, Renzo Guerrini, Dagmar Wieczorek, Laura Canafoglia, Annapurna Poduri, Christina E. Hoei-Hansen, Agathe Roubertie, Nils A Koch, Karen Müller-Schlüter, Chloe A Stutterd, Ngoc Minh Le, Pia Zacher, Constanze Heine, Sonja Walsh, Carla Marini, Federico Zara, Karl Martin Klein, Eva H. Brilstra, Guido Rubboli, Walid Fazeli, Judith Kroell-Seger, Rikke S. Møller, Dorota Hoffman-Zacharska, Michael Alber, Phillis Lakeman, Massimo Mastrangelo, Margarete Koch-Hogrebe, Ingo Helbig, Daniel Tibussek, Marketa Vlckova, Anne Destrée, Wen-Hann Tan, Haim Bassan, Dennis Lal, Patrizia Accorsi, Bert van der Zwaag, Cathrine E Gjerulfsen, Marion Gérard, Sara Matricardi, Thomas U. Mayer, Philippe Gelisse, Jong M. Rho, and Marie-Cécile Nassogne
Subjects: medicine.medical_specialty, Benign familial infantile epilepsy, business.industry, medicine.disease, Gastroenterology, Phenotype, Epilepsy, Electrophysiology, Sodium channel blocker, Internal medicine, medicine, Missense mutation, Generalized epilepsy, business, Genotype-Phenotype Correlations
Abstract: We report detailed functional analyses and genotype-phenotype correlations in 433 individuals carrying disease-causing variants in SCN8A, encoding the voltage-gated Na+ channel NaV1.6. Five different clinical subgroups could be identified: 1) Benign familial infantile epilepsy (BFIE) (n=17, normal cognition, treatable seizures), 2) intermediate epilepsy (n=36, mild ID, partially pharmacoresponsive), 3) developmental and epileptic encephalopathy (DEE, n=191, severe ID, majority pharmacoresistant), 4) generalized epilepsy (n=21, mild to moderate ID, frequently with absence seizures), and 5) affected individuals without epilepsy (n=25, mild to moderate ID). Groups 1-3 presented with early-onset (median: four months) focal or multifocal seizures and epileptic discharges, whereas the onset of seizures in group 4 was later (median: 39 months) with generalized epileptic discharges. The epilepsy was not classifiable in 143 individuals. We performed functional studies expressing missense variants in ND7/23 neuroblastoma cells and primary neuronal cultures using recombinant tetrodotoxin insensitive human NaV1.6 channels and whole-cell patch clamping. Two variants causing DEE showed a strong gain-of-function (GOF, hyperpolarising shift of steady-state activation, strongly increased neuronal firing rate), and one variant causing BFIE or intermediate epilepsy showed a mild GOF (defective fast inactivation, less increased firing). In contrast, all three variants causing generalized epilepsy induced a loss-of-function (LOF, reduced current amplitudes, depolarising shift of steady-state activation, reduced neuronal firing). Including previous studies, functional effects were known for 165 individuals. All 133 individuals carrying GOF variants had either focal (76, groups 1-3), or unclassifiable epilepsy (37), whereas 32 with LOF variants had either generalized (14), no (11) or unclassifiable (5) epilepsy; only two had DEE. Computational modeling in the GOF group revealed a significant correlation between the severity of the electrophysiological and clinical phenotypes. GOF variant carriers responded significantly better to sodium channel blockers (SCBs) than to other anti-seizure medications, and the same applied for all individuals of groups 1-3.In conclusion, our data reveal clear genotype-phenotype correlations between age at seizure onset, type of epilepsy and gain- or loss-of-function effects of SCN8A variants. Generalized epilepsy with absence seizures is the main epilepsy phenotype of LOF variant carriers and the extent of the electrophysiological dysfunction of the GOF variants is a main determinant of the severity of the clinical phenotype in focal epilepsies. Our pharmacological data indicate that SCBs present a therapeutic treatment option in early onset SCN8A-related focal epilepsy.
Published: 2021
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18. 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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19. PURA- Related Developmental and Epileptic Encephalopathy: Phenotypic and Genotypic Spectrum

Author: Dario Pruna, Theresa Grebe, Felippe Borlot, Michael J. Esser, Juan Pablo Appendino, Katherine L. Helbig, Elisa Ballardini, Casey Brew, Anne-Sophie Denommé-Pichon, Anne Ronan, Laurie A. Demmer, Usha Kini, Marta Somorai, Julie Vogt, Sébastien Moutton, Raffaella Faggioli, Julien Van-Gils, Davide Ognibene, Sara Olivotto, Sabine Grønborg, David Coman, David P. Bick, Guido Rubboli, Orrin Devinsky, Atiya S. Khan, Robyn Whitney, Christine Coubes, Caroline Nava, Karen Keough, SakkuBai R. Naidu, Lucio Giordano, Davide Colavito, Dominic Spadafore, Arnaud Isapof, Walla Al-Hertani, Antonio Vitobello, Andrea V. Andrade, Gaetano Cantalupo, Sandra Whalen, Boudewijn Gunning, Shanawaz Hussain, David Hunt, Nathan Noble, Bertrand Isidor, Beatriz Gamboni, Katrine M Johannesen, Julien Buratti, Stephanie Moortgat, Ida Cursio, Agnese Suppiej, Delphine Héron, Lía Mayorga, William Benko, Rahul Raman Singh, Cyril Mignot, Sotirios Keros, Aurore Garde, Nicola Foulds, Claudia A. L. Ruivenkamp, Elena Gardella, Barbara Scelsa, Fernanda Góes, Laurence Faivre, Richard J. Leventer, Ashley Collier, Farha Tokarz, Thomas Courtin, Klaas J. Wierenga, Xilma R. Ortiz-Gonzalez, Frédéric Tran-Mau-Them, Alejandra Mampel, Lynn Greenhalgh, Ashlea Franques, Amélie Piton, Felicia Varsalone, Marjolaine Willems, Alessandro Orsini, Diana Rodriguez, Clothilde Ormieres, Helen Stewart, Boris Keren, Austin Larson, Cathrine E. Gjerulfsen, Julie S. Cohen, Margot R.F. Reijnders, Mel Anderson, Shailesh Asakar, Rikke S. Møller, Alice Bonuccelli, Alexandra Afenjar, Claudio Graziano, Elaine Wirrell, Simona Damioli, Sangeetha Yoganathan, Devorah Segal, Ingo Helbig, Mindy H. Li, Rob P.W. Rouhl, Sarah Hicks, Allan Bayat, Holly Dubbs, Stefania Bigoni, Kelly Ratke, John Brandsema, Eva H. Brilstra, univOAK, Archive ouverte, The Danish Epilepsy Centre Filadelfia [Dianalund, Denmark], University of Southern Denmark (SDU), Maastricht University Medical Centre (MUMC), Maastricht University [Maastricht], CHU Trousseau [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Centre de référence Déficiences Intellectuelles de Causes Rares [CHU Pitié-Salpétrière], 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), Service de Génétique Cytogénétique et Embryologie [CHU Pitié-Salpêtrière], Institut du Cerveau = Paris Brain Institute (ICM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-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)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Mayo Clinic [Jacksonville], Département de pédiatrie [CHU Nantes], Centre hospitalier universitaire de Nantes (CHU Nantes), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), 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), 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, Hôpital d'Enfants [CHU Dijon], Hôpital du Bocage, Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon)-Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Equipe GAD (LNC - U1231), 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, Laboratoire de génétique des maladies rares. Pathologie moleculaire, etudes fonctionnelles et banque de données génétiques (LGMR), Université Montpellier 1 (UM1)-IFR3, Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Université Bourgogne Franche-Comté [COMUE] (UBFC), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Department of Pediatrics [Univ California San Diego] (UC San Diego), School of Medicine [Univ California San Diego] (UC San Diego), University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC)-University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), and University of Colorado Anschutz [Aurora]
Subjects: Pediatrics, medicine.medical_specialty, Socio-culturale, [SDV.GEN] Life Sciences [q-bio]/Genetics, Electroencephalography, Epilepsy, Developmental and Epileptic Encephalopathy, Intellectual disability, medicine, Genetics (clinical), feeding difficulties, [SDV.GEN]Life Sciences [q-bio]/Genetics, medicine.diagnostic_test, business.industry, fungi, medicine.disease, Hypotonia, Epileptic spasms, Neonatal hypotonia, neonatal hypotonia, Epilepsy syndromes, Cohort, epilepsy, Neurology (clinical), medicine.symptom, business
Abstract: Background and ObjectivesPurine-rich element-binding protein A (PURA) gene encodes Pur-α, a conserved protein essential for normal postnatal brain development. Recently, a PURA syndrome characterized by intellectual disability, hypotonia, epilepsy, and dysmorphic features was suggested. The aim of this study was to define and expand the phenotypic spectrum of PURA syndrome by collecting data, including EEG, from a large cohort of affected patients.MethodsData on unpublished and published cases were collected through the PURA Syndrome Foundation and the literature. Data on clinical, genetic, neuroimaging, and neurophysiologic features were obtained.ResultsA cohort of 142 patients was included. Characteristics of the PURA syndrome included neonatal hypotonia, feeding difficulties, and respiratory distress. Sixty percent of the patients developed epilepsy with myoclonic, generalized tonic-clonic, focal seizures, and/or epileptic spasms. EEG showed generalized, multifocal, or focal epileptic abnormalities. Lennox-Gastaut was the most common epilepsy syndrome. Drug refractoriness was common: 33.3% achieved seizure freedom. We found 97 pathogenic variants in PURA without any clear genotype-phenotype associations.DiscussionThe PURA syndrome presents with a developmental and epileptic encephalopathy with characteristics recognizable from neonatal age, which should prompt genetic screening. Sixty percent have drug-resistant epilepsy with focal or generalized seizures. We collected more than 90 pathogenic variants without observing overt genotype-phenotype associations.
Published: 2021
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20. 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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21. FBXO28 causes developmental and epileptic encephalopathy with profound intellectual disability

Author: Lance H. Rodan, Chelsea Chambers, Sophie Calvert, Montserrat Arellano, Elisabeth Gabau, Amy L Schneider, Jacques L. Michaud, Ariane Soldatos, Nino Spataro, M. Scott Perry, Gerarda Cappuccio, Christopher Balak, Mary D. King, Alison M. Muir, Heather C Mefford, Elsa Rossignol, Katherine L. Helbig, Carsten G. Bönnemann, Ingrid E. Scheffer, Candace T. Myers, Nicola Brunetti-Pierri, Kathleen M. Gorman, Sandra Donkervoort, Alice Basinger, Fadi F. Hamdan, Schneider, A. L., Myers, C. T., Muir, A. M., Calvert, S., Basinger, A., Perry, M. S., Rodan, L., Helbig, K. L., Chambers, C., Gorman, K. M., King, M. D., Donkervoort, S., Soldatos, A., Bonnemann, C. G., Spataro, N., Gabau, E., Arellano, M., Cappuccio, G., Brunetti Pierri, N., Rossignol, E., Hamdan, F. F., Michaud, J. L., Balak, C., Mefford, H. C., and Scheffer, I. E.
Subjects: Adult, Male, 0301 basic medicine, Drug Resistant Epilepsy, Pediatrics, medicine.medical_specialty, Microcephaly, Movement disorders, Adolescent, Encephalopathy, Mutation, Missense, Progressive myoclonus epilepsy, profound intellectual disability, Craniofacial Abnormalities, Young Adult, 03 medical and health sciences, Epilepsy, 0302 clinical medicine, Intellectual Disability, Intellectual disability, FBXO28, Humans, Medicine, developmental and epileptic encephalopathy, Child, Frameshift Mutation, Brain Diseases, SKP Cullin F-Box Protein Ligases, business.industry, Infant, Electroencephalography, Myoclonic Epilepsies, Progressive, medicine.disease, Hypotonia, Phenotype, 030104 developmental biology, Neurology, Codon, Nonsense, Child, Preschool, Female, movement disorder, Neurology (clinical), medicine.symptom, business, Epileptic Syndromes, Spasms, Infantile, 030217 neurology & neurosurgery
Abstract: Chromosome 1q41-q42 deletion syndrome is a rare cause of intellectual disability, seizures, dysmorphology, and multiple anomalies. Two genes in the 1q41-q42 microdeletion, WDR26 and FBXO28, have been implicated in monogenic disease. Patients with WDR26 encephalopathy overlap clinically with those with 1q41-q42 deletion syndrome, whereas only one patient with FBXO28 encephalopathy has been described. Seizures are a prominent feature of 1q41-q42 deletion syndrome; therefore, we hypothesized that pathogenic FBXO28 variants cause developmental and epileptic encephalopathies (DEEs). We describe nine new patients with FBXO28 pathogenic variants (four missense, including one recurrent, three nonsense, and one frameshift) and analyze all 10 known cases to delineate the phenotypic spectrum. All patients had epilepsy and 9 of 10 had DEE, including infantile spasms (3) and a progressive myoclonic epilepsy (1). Median age at seizure onset was 22.5 months (range 8 months to 5 years). Nine of 10 patients had intellectual disability, which was profound in six of nine and severe in three of nine. Movement disorders occurred in eight of 10 patients, six of 10 had hypotonia, four of 10 had acquired microcephaly, and five of 10 had dysmorphic features, albeit different to those typically seen in 1q41-q42 deletion syndrome and WDR26 encephalopathy. We distinguish FBXO28 encephalopathy from both of these disorders with more severe intellectual impairment, drug-resistant epilepsy, and hyperkinetic movement disorders.
Published: 2020
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22. Phenotypic homogeneity in childhood epilepsies evolves in gene-specific patterns across 3251 patient-years of clinical data

Author: Sarah E McKeown, Margaret O'Brien, Alex Felmeister, David Lewis-Smith, Colin A Ellis, Ingo Helbig, Katherine L. Helbig, Shiva Ganesan, Alexander K. Gonzalez, Roland Krause, Peter D. Galer, Pouya Khankhanian, and Michael C. Kaufman
Subjects: 0301 basic medicine, Male, Genetic testing, Quantitative Trait Loci, Biology, Article, 03 medical and health sciences, Genetic Heterogeneity, Prognostic markers, 0302 clinical medicine, Similarity (psychology), Human Phenotype Ontology, Genetics research, Genetics, Humans, Child, Gene, Genetics (clinical), Medical record, Electronic medical record, Infant, Diagnostic markers, Phenotype, Clinical trial, 030104 developmental biology, Evolutionary biology, Child, Preschool, Cohort, Female, Spasms, Infantile, 030217 neurology & neurosurgery
Abstract: While genetic studies of epilepsies can be performed in thousands of individuals, phenotyping remains a manual, non-scalable task. A particular challenge is capturing the evolution of complex phenotypes with age. Here, we present a novel approach, applying phenotypic similarity analysis to a total of 3251 patient-years of longitudinal electronic medical record data from a previously reported cohort of 658 individuals with genetic epilepsies. After mapping clinical data to the Human Phenotype Ontology, we determined the phenotypic similarity of individuals sharing each genetic etiology within each 3-month age interval from birth up to a maximum age of 25 years. 140 of 600 (23%) of all 27 genes and 3-month age intervals with sufficient data for calculation of phenotypic similarity were significantly higher than expect by chance. 11 of 27 genetic etiologies had significant overall phenotypic similarity trajectories. These do not simply reflect strong statistical associations with single phenotypic features but appear to emerge from complex clinical constellations of features that may not be strongly associated individually. As an attempt to reconstruct the cognitive framework of syndrome recognition in clinical practice, longitudinal phenotypic similarity analysis extends the traditional phenotyping approach by utilizing data from electronic medical records at a scale that is far beyond the capabilities of manual phenotyping. Delineation of how the phenotypic homogeneity of genetic epilepsies varies with age could improve the phenotypic classification of these disorders, the accuracy of prognostic counseling, and by providing historical control data, the design and interpretation of precision clinical trials in rare diseases.
Published: 2020

23. Current knowledge of SLC6A1-related neurodevelopmental disorders

Author: Byungchan Lim, Sumaiya Iqbal, Catherine A. Brownstein, Kimberly Goodspeed, Rikke S. Møller, Emily de los Reyes, Brandon Prentice, Katrine M Johannesen, Vincenzo Crunelli, Amber Freed, Ingo Helbig, Dianalee McKnight, Dominique Cooper, Annalisa Scimemi, Dennis Lal, Eduardo Pérez-Palma, Jingqiong Kang, Katherine L. Helbig, Arthur Stefanski, Frances C. Shaffo, Scott Demarest, and Arthur J. Campbell
Subjects: 0301 basic medicine, Review Article, Biology, gamma-Aminobutyric acid, Reuptake, GABA transporter 1, 03 medical and health sciences, Epilepsy, 0302 clinical medicine, Intellectual disability, medicine, GABA transporter, seizures, AcademicSubjects/SCI01870, SLC6A1 haploinsufficiency, neurodevelopmental disorders, General Engineering, medicine.disease, Solute carrier family, 030104 developmental biology, Autism spectrum disorder, SLC6A1-related disorders, biology.protein, AcademicSubjects/MED00310, Neuroscience, 030217 neurology & neurosurgery, medicine.drug
Abstract: Advances in gene discovery have identified genetic variants in the solute carrier family 6 member 1 gene as a monogenic cause of neurodevelopmental disorders, including epilepsy with myoclonic atonic seizures, autism spectrum disorder and intellectual disability. The solute carrier family 6 member 1 gene encodes for the GABA transporter protein type 1, which is responsible for the reuptake of the neurotransmitter GABA, the primary inhibitory neurotransmitter in the central nervous system, from the extracellular space. GABAergic inhibition is essential to counterbalance neuronal excitation, and when significantly disrupted, it negatively impacts brain development leading to developmental differences and seizures. Aggregation of patient variants and observed clinical manifestations expand understanding of the genotypic and phenotypic spectrum of this disorder. Here, we assess genetic and phenotypic features in 116 individuals with solute carrier family 6 member 1 variants, the vast majority of which are likely to lead to GABA transporter protein type 1 loss-of-function. The knowledge acquired will guide therapeutic decisions and the development of targeted therapies that selectively enhance transporter function and may improve symptoms. We analysed the longitudinal and cell type-specific expression of solute carrier family 6 member 1 in humans and localization of patient and control missense variants in a novel GABA transporter protein type 1 protein structure model. In this update, we discuss the progress made in understanding and treating solute carrier family 6 member 1-related disorders thus far, through the concerted efforts of clinicians, scientists and family support groups., Genetic variants in the SLC6A1 gene have been identified as a monogenic cause of neurodevelopmental disorders, including epilepsy with myoclonic atonic seizures, autism spectrum disorder and intellectual disability. Here, we assess the genetic and phenotypic features observed in 116 patients with SLC6A1 variants., Graphical Abstract Graphical Abstract
Published: 2020
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24. SCN3A ‐related neurodevelopmental disorder: A spectrum of epilepsy and brain malformation

Author: Thuy Anh Vu, Sally Ackermann, Andrew E. Fry, Seok Kyu Kang, Shelagh Joss, Katrien Stouffs, Satoko Miyatake, Katherine A. Fawcett, Ethan M. Goldberg, Elena Parrini, Natalie Hauser, Anna E. Jansen, Daniela T. Pilz, Daphna Marom, Adeline Jacquinet, Katherine L. Helbig, Yuh Fujiwara, Natalie Lippa, Orit Reish, Ingo Helbig, Bruria Ben-Zeev, Shraddha Srinivasan, Pradeep Vasudevan, Renzo Guerrini, Careni Spencer, Lieve Verstraete, Agnieszka Charzewska, Christopher H. Thompson, Jérôme Clatot, Jennifer A. Kearney, David R. FitzPatrick, Haim Bassan, Victoria Harrison, Naomichi Matsumoto, Tariq Zaman, Dorota Hoffman-Zacharska, Clinical sciences, Medical Genetics, Reproduction and Genetics, Physiotherapy, Human Physiology and Anatomy, Pediatrics, Public Health Sciences, Mental Health and Wellbeing research group, and Neurogenetics
Subjects: 0301 basic medicine, Adult, Male, Adolescent, Biology, Sodium Channels, Article, 03 medical and health sciences, Epilepsy, SCN3A, 0302 clinical medicine, Neurodevelopmental disorder, Fetus, Channelopathy, Intellectual disability, medicine, NAV1.3 Voltage-Gated Sodium Channel, Missense mutation, Humans, Child, Sodium channel, Brain, Genetic Variation, Infant, medicine.disease, Electrophysiology, 030104 developmental biology, HEK293 Cells, Neurology, Neurodevelopmental Disorders, Child, Preschool, Female, Neurology (clinical), Neuroscience, 030217 neurology & neurosurgery
Abstract: Objective\ud \ud Pathogenic variants in SCN3A , encoding the voltage‐gated sodium channel subunit Nav1.3, cause severe childhood‐onset epilepsy and malformation of cortical development. Here, we define the spectrum of clinical, genetic, and neuroimaging features of SCN3A ‐related neurodevelopmental disorder.\ud Methods\ud \ud Patients were ascertained via an international collaborative network. We compared sodium channels containing wild‐type vs. variant Nav1.3 subunits co‐expressed with β1 and β2 subunits using whole‐cell voltage clamp electrophysiological recordings in a heterologous mammalian system (HEK‐293 T cells).\ud Results\ud \ud Of 22 patients with pathogenic SCN3A variants, most had treatment‐resistant epilepsy beginning in the first year of life (16/21, 76%; median onset, 2 weeks), with severe or profound developmental delay (15/20; 75%). Many, but not all (15/19; 79%), exhibited malformations of cortical development. Pathogenic variants clustered in transmembrane segments 4–6 of domains II‐IV. Most pathogenic missense variants tested (10/11; 91%) displayed gain of channel function, with increased persistent current and/or a leftward shift in the voltage dependence of activation, and all variants associated with malformation of cortical development exhibited gain of channel function. One variant (p.Ile1468Arg) exhibited mixed effects, with gain and partial loss of function. Two variants demonstrated loss of channel function.\ud Interpretation\ud \ud Our study defines SCN3A‐ related neurodevelopmental disorder along a spectrum of severity, but typically including epilepsy and severe or profound developmental delay/intellectual disability. Malformations of cortical development are a characteristic feature of this unusual channelopathy syndrome, present in over 75% of affected individuals. Gain of function at the channel level in developing neurons is likely an important mechanism of disease pathogenesis.
Published: 2020

25. Novel Missense

Author: Géza Berecki, Cara M. Skraban, Samuel F. Berkovic, Bronwyn E. Grinton, Katherine L. Helbig, Tyson L Ware, Eric D. Marsh, and Steven Petrou
Subjects: Male, medicine.medical_specialty, Cerebellum, gain of function, Developmental Disabilities, Mutation, Missense, CACNA1G mutation, Deep cerebellar nuclei, medicine.disease_cause, Article, Catalysis, lcsh:Chemistry, Inorganic Chemistry, Calcium Channels, T-Type, Internal medicine, medicine, Missense mutation, Humans, Physical and Theoretical Chemistry, developmental and epileptic encephalopathy, lcsh:QH301-705.5, Molecular Biology, Spectroscopy, Mutation, Cerebellar ataxia, Calcium channel, voltage-dependent T-type calcium channel, deep cerebellar nuclei, Organic Chemistry, General Medicine, Phenotype, Computer Science Applications, Endocrinology, medicine.anatomical_structure, lcsh:Biology (General), lcsh:QD1-999, loss of function, Cerebellar atrophy, Female, medicine.symptom, Spasms, Infantile
Abstract: The CACNA1G gene encodes the low-voltage-activated Cav3.1 channel, which is expressed in various areas of the CNS, including the cerebellum. We studied two missense CACNA1G variants, p.L208P and p.L909F, and evaluated the relationships between the severity of Cav3.1 dysfunction and the clinical phenotype. The presentation was of a developmental and epileptic encephalopathy without evident cerebellar atrophy. Both patients exhibited axial hypotonia, developmental delay, and severe to profound cognitive impairment. The patient with the L909F mutation had initially refractory seizures and cerebellar ataxia, whereas the L208P patient had seizures only transiently but was overall more severely affected. In transfected mammalian cells, we determined the biophysical characteristics of L208P and L909F variants, relative to the wild-type channel and a previously reported gain-of-function Cav3.1 variant. The L208P mutation shifted the activation and inactivation curves to the hyperpolarized direction, slowed the kinetics of inactivation and deactivation, and reduced the availability of Ca2+ current during repetitive stimuli. The L909F mutation impacted channel function less severely, resulting in a hyperpolarizing shift of the activation curve and slower deactivation. These data suggest that L909F results in gain-of-function, whereas L208P exhibits mixed gain-of-function and loss-of-function effects due to opposing changes in the biophysical properties. Our study expands the clinical spectrum associated with CACNA1G mutations, corroborating further the causal association with distinct complex phenotypes.
Published: 2020

26. Histone H3.3 beyond cancer: Germline mutations in

Author: Laura, Bryant, Dong, Li, Samuel G, Cox, Dylan, Marchione, Evan F, Joiner, Khadija, Wilson, Kevin, Janssen, Pearl, Lee, Michael E, March, Divya, Nair, Elliott, Sherr, Brieana, Fregeau, Klaas J, Wierenga, Alexandrea, Wadley, Grazia M S, Mancini, Nina, Powell-Hamilton, Jiddeke, van de Kamp, Theresa, Grebe, John, Dean, Alison, Ross, Heather P, Crawford, Zoe, Powis, Megan T, Cho, Marcia C, Willing, Linda, Manwaring, Rachel, Schot, Caroline, Nava, Alexandra, Afenjar, Davor, Lessel, Matias, Wagner, Thomas, Klopstock, Juliane, Winkelmann, Claudia B, Catarino, Kyle, Retterer, Jane L, Schuette, Jeffrey W, Innis, Amy, Pizzino, Sabine, Lüttgen, Jonas, Denecke, Tim M, Strom, Kristin G, Monaghan, Zuo-Fei, Yuan, Holly, Dubbs, Renee, Bend, Jennifer A, Lee, Michael J, Lyons, Julia, Hoefele, Roman, Günthner, Heiko, Reutter, Boris, Keren, Kelly, Radtke, Omar, Sherbini, Cameron, Mrokse, Katherine L, Helbig, Sylvie, Odent, Benjamin, Cogne, Sandra, Mercier, Stephane, Bezieau, Thomas, Besnard, Sebastien, Kury, Richard, Redon, Karit, Reinson, Monica H, Wojcik, Katrin, Õunap, Pilvi, Ilves, A Micheil, Innes, Kristin D, Kernohan, Gregory, Costain, M Stephen, Meyn, David, Chitayat, Elaine, Zackai, Anna, Lehman, Hilary, Kitson, Martin G, Martin, Julian A, Martinez-Agosto, Stan F, Nelson, Christina G S, Palmer, Jeanette C, Papp, Neil H, Parker, Janet S, Sinsheimer, Eric, Vilain, Jijun, Wan, Amanda J, Yoon, Allison, Zheng, Elise, Brimble, Giovanni Battista, Ferrero, Francesca Clementina, Radio, Diana, Carli, Sabina, Barresi, Alfredo, Brusco, Marco, Tartaglia, Jennifer Muncy, Thomas, Luis, Umana, Marjan M, Weiss, Garrett, Gotway, K E, Stuurman, Michelle L, Thompson, Kirsty, McWalter, Constance T R M, Stumpel, Servi J C, Stevens, Alexander P A, Stegmann, Kristian, Tveten, Arve, Vøllo, Trine, Prescott, Christina, Fagerberg, Lone Walentin, Laulund, Martin J, Larsen, Melissa, Byler, Robert Roger, Lebel, Anna C, Hurst, Joy, Dean, Samantha A, Schrier Vergano, Jennifer, Norman, Saadet, Mercimek-Andrews, Juanita, Neira, Margot I, Van Allen, Nicola, Longo, Elizabeth, Sellars, Raymond J, Louie, Sara S, Cathey, Elly, Brokamp, Delphine, Heron, Molly, Snyder, Adeline, Vanderver, Celeste, Simon, Xavier, de la Cruz, Natália, Padilla, J Gage, Crump, Wendy, Chung, Benjamin, Garcia, Hakon H, Hakonarson, and Elizabeth J, Bhoj
Subjects: endocrine system, SciAdv r-articles, Forkhead Transcription Factors, Neurodegenerative Diseases, Zebrafish Proteins, Histones, fluids and secretions, mental disorders, Genetics, Animals, Humans, Molecular Biology, reproductive and urinary physiology, Germ-Line Mutation, Zebrafish, Research Articles, Research Article
Abstract: Germ line mutations in H3F3A and H3F3B cause a previously unidentified neurodevelopmental syndrome., Although somatic mutations in Histone 3.3 (H3.3) are well-studied drivers of oncogenesis, the role of germline mutations remains unreported. We analyze 46 patients bearing de novo germline mutations in histone 3 family 3A (H3F3A) or H3F3B with progressive neurologic dysfunction and congenital anomalies without malignancies. Molecular modeling of all 37 variants demonstrated clear disruptions in interactions with DNA, other histones, and histone chaperone proteins. Patient histone posttranslational modifications (PTMs) analysis revealed notably aberrant local PTM patterns distinct from the somatic lysine mutations that cause global PTM dysregulation. RNA sequencing on patient cells demonstrated up-regulated gene expression related to mitosis and cell division, and cellular assays confirmed an increased proliferative capacity. A zebrafish model showed craniofacial anomalies and a defect in Foxd3-derived glia. These data suggest that the mechanism of germline mutations are distinct from cancer-associated somatic histone mutations but may converge on control of cell proliferation.
Published: 2020

27. Histone H3.3 beyond cancer: Germline mutations in Histone 3 Family 3A and 3B cause a previously unidentified neurodegenerative disorder in 46 patients

Author: Thomas Besnard, Kristian Tveten, Hilary F Kitson, Jennifer A. Lee, Brieana Fregeau, Rachel Schot, Khadija Wilson, Katrin Õunap, Juliane Winkelmann, Anna Lehman, Nicola Longo, Servi J. C. Stevens, Megan T. Cho, Christina G.S. Palmer, Causes Study, Giovanni Battista Ferrero, Joy Dean, Lone W. Laulund, Grazia M.S. Mancini, Matias Wagner, Martin G. Martin, Sabine Lüttgen, Elizabeth J. Bhoj, Amanda J. Yoon, Thomas Klopstock, Janet S. Sinsheimer, Eric Vilain, Sébastien Küry, Francesca Clementina Radio, Jiddeke M. van de Kamp, Cameron Mrokse, Hakon Hakonarson, Samuel G. Cox, Jeanette C. Papp, Margot I. Van Allen, Raymond J. Louie, Constance T. R. M. Stumpel, Evan F. Joiner, Juanita Neira, Arve Vøllo, Amy Pizzino, Kelly Radtke, Celeste Simon, Michelle L. Thompson, Allison Zheng, Omar Sherbini, Marcia C. Willing, Tim M. Strom, Benjamin Garcia, Sara S. Cathey, Theresa A. Grebe, Dong Li, Marjan M. Weiss, Marco Tartaglia, Laura M Bryant, Sandra Mercier, Katherine L. Helbig, Martin Jakob Larsen, Ddd Study, Alexandrea Wadley, Alexander P.A. Stegmann, Sabina Barresi, A. Micheil Innes, Elaine H. Zackai, Gregory Costain, Davor Lessel, Molly Snyder, Heather P. Crawford, Richard Redon, Pearl Lee, Melissa Byler, Holly Dubbs, J. Gage Crump, K. E. Stuurman, Boris Keren, Stéphane Bézieau, Stan F. Nelson, Kristin G. Monaghan, Michael J. Lyons, Jeffrey W. Innis, Anna C.E. Hurst, Elizabeth A. Sellars, Samantha A. Schrier Vergano, Saadet Mercimek-Andrews, Monica H. Wojcik, Alison Ross, Heiko Reutter, Zuo-Fei Yuan, Dylan M. Marchione, Renee Bend, Diana Carli, Zöe Powis, Neil H. Parker, Jennifer Muncy Thomas, Luis A. Umaña, Adeline Vanderver, Julia Hoefele, Linda Manwaring, Christina Fagerberg, Elly Brokamp, M. Stephen Meyn, Pilvi Ilves, Xavier de la Cruz, Nina Powell-Hamilton, Caroline Nava, Garrett Gotway, Karit Reinson, Kristin D. Kernohan, Jennifer Norman, Alexandra Afenjar, Benjamin Cogné, Delphine Héron, Roman Günthner, Alfredo Brusco, John Dean, Kevin A. Janssen, Robert Roger Lebel, Divya Nair, Jijun Wan, Julian A. Martinez-Agosto, Elliott H. Sherr, Kyle Retterer, Claudia B. Catarino, Michael E. March, Natalia Padilla, Elise Brimble, Sylvie Odent, Jane L. Schuette, David Chitayat, Klaas J. Wierenga, Kirsty McWalter, Trine Prescott, Jonas Denecke, Wendy K. Chung, Human genetics, Amsterdam Neuroscience - Complex Trait Genetics, Amsterdam Gastroenterology Endocrinology Metabolism, Klinische Genetica, MUMC+: DA KG Polikliniek (9), RS: GROW - R4 - Reproductive and Perinatal Medicine, MUMC+: DA KG Lab Centraal Lab (9), and Clinical Genetics
Subjects: metabolism [Zebrafish Proteins], RESIDUE, metabolism [Histones], GENES, Somatic cell, CODE, cancer mutation, histone, Biology, VARIANTS, medicine.disease_cause, progressive neurologic dysfunction, Histones, 03 medical and health sciences, Histone H3, 0302 clinical medicine, Germline mutation, SDG 3 - Good Health and Well-being, histone, neurodevelopmental disorder, progressive neurologic dysfunction, congenital anomalies, cancer mutation, medicine, Animals, Humans, H3-3A protein, human, metabolism [Zebrafish], TRANSCRIPTION, PHOSPHORYLATION, Gene, Zebrafish, Germ-Line Mutation, 030304 developmental biology, Genetics, genetics [Zebrafish], 0303 health sciences, Multidisciplinary, foxd3 protein, zebrafish, congenital anomalies, Forkhead Transcription Factors, Zebrafish Proteins, biology.organism_classification, genetics [Histones], neurodevelopmental disorder, H3F3B, Histone, genetics [Forkhead Transcription Factors], genetics [Neurodegenerative Diseases], biology.protein, ddc:500, Carcinogenesis, 030217 neurology & neurosurgery
Abstract: Germ line mutations in H3F3A and H3F3B cause a previously unidentified neurodevelopmental syndrome. Although somatic mutations in Histone 3.3 (H3.3) are well-studied drivers of oncogenesis, the role of germline mutations remains unreported. We analyze 46 patients bearing de novo germline mutations in histone 3 family 3A (H3F3A) or H3F3B with progressive neurologic dysfunction and congenital anomalies without malignancies. Molecular modeling of all 37 variants demonstrated clear disruptions in interactions with DNA, other histones, and histone chaperone proteins. Patient histone posttranslational modifications (PTMs) analysis revealed notably aberrant local PTM patterns distinct from the somatic lysine mutations that cause global PTM dysregulation. RNA sequencing on patient cells demonstrated up-regulated gene expression related to mitosis and cell division, and cellular assays confirmed an increased proliferative capacity. A zebrafish model showed craniofacial anomalies and a defect in Foxd3-derived glia. These data suggest that the mechanism of germline mutations are distinct from cancer-associated somatic histone mutations but may converge on control of cell proliferation
Published: 2020
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28. Damaging de novo missense variants in EEF1A2lead to a developmental and degenerative epileptic-dyskinetic encephalopathy

Author: Laurine Perrin, Sha Tang, Brandon S. Guida, Tjitske Kleefstra, Marjolein H. Willemsen, Heather Stickney, Michael C. Kruer, Keri Ramsey, Heather C Mefford, Lynette G. Sadleir, Bobby P. C. Koeleman, Evelyn Sattlegger, Angela E. Lin, Sara A. Lewis, Marcello Scala, Sergio Padilla-Lopez, Luis O. Rohena, Joaquim Sa, Marie Laure Mathieu, Floor E. Jansen, Joy Y. Sebe, David W. Raible, Giorgio Casari, Gemma L. Carvill, Ingrid E. Scheffer, Paul A. Caruso, Robert Huether, Mariasavina Severino, Candace T. Myers, Eva H. Brilstra, Ashwin A. Bhandiwad, Katherine L. Helbig, Somayeh Bakhtiari, Sehribani Ulusoy Oktay, Gaetan Lesca, Vinodh Narayanan, Georgina Hollingsworth, Tyler N. Kruer, Christel Depienne, Valeria Capra, Pasquale Striano, Timothy Feyma, Deepak Gill, Andrea Accogli, Caroline Nava, Carvill, G. L., Helbig, K. L., Myers, C. T., Scala, M., Huether, R., Lewis, S., Kruer, T. N., Guida, B. S., Bakhtiari, S., Sebe, J., Tang, S., Stickney, H., Oktay, S. U., Bhandiwad, A. A., Ramsey, K., Narayanan, V., Feyma, T., Rohena, L. O., Accogli, A., Severino, M., Hollingsworth, G., Gill, D., Depienne, C., Nava, C., Sadleir, L. G., Caruso, P. A., Lin, A. E., Jansen, F. E., Koeleman, B., Brilstra, E., Willemsen, M. H., Kleefstra, T., Sa, J., Mathieu, M. -L., Perrin, L., Lesca, G., Striano, P., Casari, G., Scheffer, I. E., Raible, D., Sattlegger, E., Capra, V., Padilla-Lopez, S., Mefford, H. C., and Kruer, M. C.
Subjects: Adult, Male, de novo, Heterozygote, Adolescent, Encephalopathy, Choreoathetosis, Mutation, Missense, EEF1A2, Haploinsufficiency, Biology, Article, 03 medical and health sciences, Epilepsy, All institutes and research themes of the Radboud University Medical Center, Peptide Elongation Factor 1, Genetics, medicine, Missense mutation, Humans, Child, Genetics (clinical), 030304 developmental biology, Dystonia, 0303 health sciences, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], 030305 genetics & heredity, Genetic Complementation Test, medicine.disease, yeast complementation assay, Protein Structure, Tertiary, dyskinesia, Child, Preschool, epilepsy, Cerebellar atrophy, Epilepsy, Generalized, Female, medicine.symptom, Rare cancers Radboud Institute for Health Sciences [Radboudumc 9]
Abstract: Heterozygous de novo variants in the eukaryotic elongation factor EEF1A2 have previously been described in association with intellectual disability and epilepsy but never functionally validated. Here we report 14 new individuals with heterozygous EEF1A2 variants. We functionally validate multiple variants as protein-damaging using heterologous expression and complementation analysis. Our findings allow us to confirm multiple variants as pathogenic and broaden the phenotypic spectrum to include dystonia/choreoathetosis, and in some cases a degenerative course with cerebral and cerebellar atrophy. Pathogenic variants appear to act via a haploinsufficiency mechanism, disrupting both the protein synthesis and integrated stress response functions of EEF1A2. Our studies provide evidence that EEF1A2 is highly intolerant to variation and that de novo pathogenic variants lead to an epileptic-dyskinetic encephalopathy with both neurodevelopmental and neurodegenerative features. Developmental features may be driven by impaired synaptic protein synthesis during early brain development while progressive symptoms may be linked to an impaired ability to handle cytotoxic stressors.
Published: 2020

29. The ClinGen Epilepsy Gene Curation Expert Panel—Bridging the divide between clinical domain knowledge and formal gene curation criteria

Author: Rebecca K. Siegert, Carrie Anne Barry, Kristen Park, Maria Roberta Cilio, Bekim Sadikovic, Ghayda M. Mirzaa, David A. Dyment, Ingo Helbig, Annapurna Poduri, Tristan T. Sands, Karl Martin Klein, Courtney Thaxton, Jacy L. Wagnon, Erin Rooney Riggs, Erika Axeen, Pasquale Striano, Tanya Bardakjian, Katherine L. Helbig, Heather C Mefford, Elizabeth Butler, Khalida Liaquat, Andrew R. Grant, UCL - SSS/IREC/PEDI - Pôle de Pédiatrie, and UCL - (SLuc) Service de neurologie pédiatrique
Subjects: ClinGen/Clinical Genome Resource, 0301 basic medicine, Disease, Computational biology, Biology, Article, gene–disease association, 03 medical and health sciences, Epilepsy, 0302 clinical medicine, clinical validity, Genetics, medicine, Humans, Genetic Testing, epilepsy, epileptic encephalopathy, Gene, Genetics (clinical), Genetic testing, Disease entity, medicine.diagnostic_test, medicine.disease, Phenotype, 030104 developmental biology, Gene selection, Seizure Disorders, Mutation, Gene-disease association, Domain knowledge, 030217 neurology & neurosurgery
Abstract: The field of epilepsy genetics is advancing rapidly and epilepsy is emerging as a frequent indication for diagnostic genetic testing. Within the larger ClinGen framework, the ClinGen Epilepsy Gene Curation Expert Panel is tasked with connecting two increasingly separate fields: the domain of traditional clinical epileptology, with its own established language and classification criteria, and the rapidly evolving area of diagnostic genetic testing that adheres to formal criteria for gene and variant curation. We identify critical components unique to the epilepsy gene curation effort, including: (1) precise phenotype definitions within existing disease and phenotype ontologies; (2) consideration of when epilepsy should be curated as a distinct disease entity; (3) strategies for gene selection; and (4) emerging rules for evaluating functional models for seizure disorders. Given that de novo variants play a prominent role in many of the epilepsies, sufficient genetic evidence is often awarded early in the curation process. Therefore, the emphasis of gene curation is frequently shifted towards an iterative precuration process to better capture phenotypic associations. We demonstrate that within the spectrum of neurodevelopmental disorders, gene curation for epilepsy-associated genes is feasible and suggest epilepsy-specific conventions, laying the groundwork for a curation process of all major epilepsy-associated genes.
Published: 2018
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30. TANGO2: expanding the clinical phenotype and spectrum of pathogenic variants

Author: Alison M. Muir, Dianne Laboy Cintrón, Katherine H. Kim, Amber Begtrup, Peter I. Karachunski, Almuth Caliebe, Heather C Mefford, Amy Lacroix, J. Lawrence Merritt, Kirsty McWalter, Angela Sun, Sharon F. Suchy, Barbara K. Burton, Ingo Helbig, René Santer, Joline C. Dalton, Dmitriy Niyazov, Rachel Westman, Ganka Douglas, Leah Fleming, Hiltrud Muhle, Kristin G. Monaghan, Alice Basinger, Katherine L. Helbig, Jenny Thies, Kolja Becker, Manuela Pendziwiat, Can Ficicioglu, Megan T. Cho, Jennifer N. Dines, Francisca Millan, and Katie Golden-Grant
Subjects: Male, 0301 basic medicine, Adolescent, DNA Copy Number Variations, Genotype, Developmental Disabilities, Encephalopathy, developmental delay DNA copy-number variation, 030105 genetics & heredity, Compound heterozygosity, Bioinformatics, Article, 03 medical and health sciences, Epilepsy, Genotype-phenotype distinction, Seizures, Intellectual Disability, Intellectual disability, medicine, Humans, Exome, Family, intragenic deletion, Child, Genetics (clinical), Exome sequencing, Brain Diseases, business.industry, Aryl Hydrocarbon Receptor Nuclear Translocator, Correction, medicine.disease, Phenotype, Pedigree, 3. Good health, 030104 developmental biology, Child, Preschool, epilepsy, Female, business, exome sequencing
Abstract: Purpose TANGO2-related disorders were first described in 2016 and prior to this publication, only 15 individuals with TANGO2-related disorder were described in the literature. Primary features include metabolic crisis with rhabdomyolysis, encephalopathy, intellectual disability, seizures, and cardiac arrhythmias. We assess whether genotype and phenotype of TANGO2-related disorder has expanded since the initial discovery and determine the efficacy of exome sequencing (ES) as a diagnostic tool for detecting variants. Methods We present a series of 14 individuals from 11 unrelated families with complex medical and developmental histories, in whom ES or microarray identified compound heterozygous or homozygous variants in TANGO2. Results The initial presentation of patients with TANGO2-related disorders can be variable, including primarily neurological presentations. We expand the phenotype and genotype for TANGO2, highlighting the variability of the disorder. Conclusion TANGO2-related disorders can have a more diverse clinical presentation than previously anticipated. We illustrate the utility of routine ES data reanalysis whereby discovery of novel disease genes can lead to a diagnosis in previously unsolved cases and the need for additional copy-number variation analysis when ES is performed.
Published: 2018

31. Diagnostic exome sequencing identifies GLI2 haploinsufficiency and chromosome 20 uniparental disomy in a patient with developmental anomalies

Author: Honey Nagakura, Katherine L. Helbig, Samin A. Sajan, Zöe Powis, LaDonna Immken, Wendy Alcaraz, and Sha Tang
Subjects: 0301 basic medicine, Genetics, congenital, hereditary, and neonatal diseases and abnormalities, uniparental disomy, business.industry, GLI2, Case Report, General Medicine, Case Reports, medicine.disease, developmental anomalies, Uniparental disomy, diagnostic exome sequencing, 03 medical and health sciences, 030104 developmental biology, Medicine, Chromosome 20, business, Haploinsufficiency, Exome sequencing
Abstract: Key Clinical Message Clinical diagnostic exome sequencing (DES) is currently infrequently used for detecting uniparental disomy (UPD). We present a patient with a dual diagnosis of GLI2 haploinsufficiency as well as UPD of chromosome 20, both identified through DES. We therefore recommend routine UPD analysis during DES to identify this genetic aberration.
Published: 2018

32. Genetics of Epilepsy in the Era of Precision Medicine: Implications for Testing, Treatment, and Genetic Counseling

Author: Katherine L. Helbig, Lacey Smith, and Beth Rosen Sheidley
Subjects: 0301 basic medicine, Genetics, education.field_of_study, business.industry, Genetic heterogeneity, Genetic counseling, Population, General Medicine, medicine.disease, Precision medicine, 03 medical and health sciences, Epilepsy, 030104 developmental biology, 0302 clinical medicine, Clinical genetic, Medicine, business, education, Genetic diagnosis, 030217 neurology & neurosurgery, Gene Discovery
Abstract: Epilepsy is among the most common neurological diseases, affecting 65 million people worldwide. Recent revisions to the classification of epilepsies by the International League Against Epilepsy (ILAE) reflect a growing awareness of genetic contributions to epilepsy. Research in epilepsy genetics has begun to look beyond gene discovery to the horizon of genotype-driven precision medicine. During the past 5 years, the advent of next-generation sequencing has led to exponential growth in the discovery of epilepsy-related genes. The yield of clinically available genetic tests for patients with epilepsy may be as high as 50%, particularly among patients with early-onset epileptic encephalopathy (EOEE). Among patients with early-life epilepsies who have a genetic diagnosis, de novo pathogenic variants are most frequently observed, and rates of somatic mosaicism among both patients and parents are higher than initially anticipated. Phenotypic heterogeneity is quite broad for many epilepsy-related genes, and genotype-phenotype correlations continue to prove complex and at times challenging. With a focus on early-life epilepsies, we review recent highlights from the literature regarding gene discovery, approaches to and outcomes of clinical genetic evaluation, and contemporary efforts toward precision treatment. We also address genetic counseling issues of relevance for this population.
Published: 2018
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33. Mutations in PMPCB Encoding the Catalytic Subunit of the Mitochondrial Presequence Protease Cause Neurodegeneration in Early Childhood

Author: F.-Nora Vögtle, Carolyn F. Delto, Hiltrud Muhle, Nils Burger, Marisa W. Friederich, Johanna A. Jähn, Ingo Helbig, Audrey Burnett, Maie Walsh, Naomichi Matsumoto, Cansu Kücükköse, Björn Brändl, Franz-Josef Müller, Hung-Chun Yu, Andreas van Baalen, Deepali N. Shinde, Austin Larson, Susan M. White, Alice Basinger, Noriko Miyake, Oliver Keminer, Ulrich Stephani, Manuela Pendziwiat, Dirk Mossmann, Lisa Myketin, Katherine L. Helbig, Mark A. Lovell, Johan L.K. Van Hove, and Publica
Subjects: Iron-Sulfur Proteins, Male, 0301 basic medicine, Saccharomyces cerevisiae Proteins, Mitochondrial disease, Induced Pluripotent Stem Cells, Respiratory chain, Saccharomyces cerevisiae, Mitochondrion, medicine.disease_cause, Proto-Oncogene Mas, Article, Electron Transport, 03 medical and health sciences, Catalytic Domain, Genetics, medicine, Humans, Child, PMPCB, Genetics (clinical), Mutation, biology, Neurodegeneration, Metalloendopeptidases, Dermis, Fibroblasts, medicine.disease, Magnetic Resonance Imaging, Mitochondria, Pedigree, Cell biology, 030104 developmental biology, Child, Preschool, Nerve Degeneration, Frataxin, biology.protein, Female, Biogenesis
Abstract: Mitochondrial disorders causing neurodegeneration in childhood are genetically heterogeneous, and the underlying genetic etiology remains unknown in many affected individuals. We identified biallelic variants in PMPCB in individuals of four families including one family with two affected siblings with neurodegeneration and cerebellar atrophy. PMPCB encodes the catalytic subunit of the essential mitochondrial processing protease (MPP), which is required for maturation of the majority of mitochondrial precursor proteins. Mitochondria isolated from two fibroblast cell lines and induced pluripotent stem cells derived from one affected individual and differentiated neuroepithelial stem cells showed reduced PMPCB levels and accumulation of the processing intermediate of frataxin, a sensitive substrate for MPP dysfunction. Introduction of the identified PMPCB variants into the homologous S. cerevisiae Mas1 protein resulted in a severe growth and MPP processing defect leading to the accumulation of mitochondrial precursor proteins and early impairment of the biogenesis of iron-sulfur clusters, which are indispensable for a broad range of crucial cellular functions. Analysis of biopsy materials of an affected individual revealed changes and decreased activity in iron-sulfur cluster-containing respiratory chain complexes and dysfunction of mitochondrial and cytosolic Fe-S cluster-dependent enzymes. We conclude that biallelic mutations in PMPCB cause defects in MPP proteolytic activity leading to dysregulation of iron-sulfur cluster biogenesis and triggering a complex neurological phenotype of neurodegeneration in early childhood.
Published: 2018
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34. Mutations in SCN3A cause early infantile epileptic encephalopathy

Author: A. G. Christina Bergqvist, Katherine L. Helbig, Suzanne D. DeBrosse, Ethan M. Goldberg, Tariq Zaman, Livija Medne, Ivana Babić Božović, Aleš Maver, Kimberly Wallis, Borut Peterlin, Xiaohong Zhang, and Ingo Helbig
Subjects: 0301 basic medicine, Nervous system, Genetics, Transfection, Biology, Early Infantile Epileptic Encephalopathy, 03 medical and health sciences, SCN3A, 030104 developmental biology, 0302 clinical medicine, medicine.anatomical_structure, Neurology, SCN1B, medicine, Missense mutation, Neurology (clinical), Patch clamp, Gene, 030217 neurology & neurosurgery
Abstract: Objective Voltage-gated sodium (Na+) channels underlie action potential generation and propagation and hence are central to the regulation of excitability in the nervous system. Mutations in the genes SCN1A, SCN2A, and SCN8A, encoding the Na+ channel pore-forming (α) subunits Nav1.1, 1.2, and 1.6, respectively, and SCN1B, encoding the accessory subunit β1, are established causes of genetic epilepsies. SCN3A, encoding Nav1.3, is known to be highly expressed in brain, but has not previously been linked to early infantile epileptic encephalopathy. Here, we describe a cohort of four patients with epileptic encephalopathy and heterozygous de novo missense variants in SCN3A (p.Ile875Thr in two cases, p.Pro1333Leu, and p.Val1769Ala).
Published: 2018
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35. Correction: Candidate-gene criteria for clinical reporting: diagnostic exome sequencing identifies altered candidate genes among 8% of patients with undiagnosed diseases

Author: Kelly D. Farwell Hagman, Deepali N. Shinde, Cameron Mroske, Erica Smith, Kelly Radtke, Layla Shahmirzadi, Dima El-Khechen, Zöe Powis, Elizabeth C. Chao, Wendy A. Alcaraz, Katherine L. Helbig, Samin A. Sajan, Mari Rossi, Hsiao-Mei Lu, Robert Huether, Shuwei Li, Sitao Wu, Mark E. Nuñes, and Sha Tang
Subjects: novel genetic etiologies, Genetic Diseases, Inborn, Correction, High-Throughput Nucleotide Sequencing, clinical diagnostic exome sequencing, gene–disease relationships, novel disease genes, Databases, Genetic, Mutation, Exome Sequencing, Humans, Exome, Original Research Article, candidate genes, Genetics (clinical), Genetic Association Studies
Abstract: Purpose: Diagnostic exome sequencing (DES) is now a commonly ordered test for individuals with undiagnosed genetic disorders. In addition to providing a diagnosis for characterized diseases, exome sequencing has the capacity to uncover novel candidate genes for disease. Methods: Family-based DES included analysis of both characterized and novel genetic etiologies. To evaluate candidate genes for disease in the clinical setting, we developed a systematic, rule-based classification schema. Results: Testing identified a candidate gene among 7.7% (72/934) of patients referred for DES; 37 (4.0%) and 35 (3.7%) of the genes received evidence scores of “candidate” and “suspected candidate,” respectively. A total of 71 independent candidate genes were reported among the 72 patients, and 38% (27/71) were subsequently corroborated in the peer-reviewed literature. This rate of corroboration increased to 51.9% (27/52) among patients whose gene was reported at least 12 months previously. Conclusions: Herein, we provide transparent, comprehensive, and standardized scoring criteria for the clinical reporting of candidate genes. These results demonstrate that DES is an integral tool for genetic diagnosis, especially for elucidating the molecular basis for both characterized and novel candidate genetic etiologies. Gene discoveries also advance the understanding of normal human biology and more common diseases. Genet Med 19 2, 224–235.
Published: 2018

36. De Novo Missense Mutations in DHX30 Impair Global Translation and Cause a Neurodevelopmental Disorder

Author: Naomi Meeks, Stefan Kindler, Anya Revah-Politi, Alexander P.A. Stegmann, Vinodh Narayanan, Dominique Bonneau, Claudia Schob, Jill A. Rosenfeld, Jennifer E. Posey, Tim M. Strom, LaDonna Immken, Tjitske Kleefstra, Jolanda H. Schieving, Katherine L. Helbig, Estelle Colin, Magalie Barth, Tamar Harel, Matthew J. Huentelman, James R. Lupski, Benjamin Cogné, Han G. Brunner, Yaping Yang, Sébastien Küry, Jenny Morton, Erica H. Gerkes, Keri Ramsey, Marine Tessarech, Zeynep Coban-Akdemir, Shimon Edvardson, Hans-Jürgen Kreienkamp, Nelly Oundjian, Davor Lessel, Christian Kubisch, Thomas Besnard, Jonas Denecke, Orly Elpeleg, Ana M. Claasen, Kelsey Zegar, Mohammad K. Eldomery, Sandra Mercier, Margot R.F. Reijnders, Stéphane Bézieau, Univ Angers, Okina, MUMC+: DA KG Lab Centraal Lab (9), Klinische Genetica, RS: GROW - R4 - Reproductive and Perinatal Medicine, MUMC+: DA Klinische Genetica (5), Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), and Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Central Nervous System, Male, DISRUPTION, INTELLECTUAL DISABILITY, Developmental Disabilities, PROTEIN, DISEASE, 0302 clinical medicine, Neurodevelopmental disorder, Intellectual disability, Missense mutation, Global developmental delay, Amino Acids, Child, Genetics (clinical), Genetics, Adenosine Triphosphatases, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, Translation (biology), Disorders of movement Donders Center for Medical Neuroscience [Radboudumc 3], 3. Good health, FAMILY, Child, Preschool, Female, RNA Helicases, MODULE, Adolescent, Mutation, Missense, RNA GRANULES, Biology, Article, Cell Line, 03 medical and health sciences, Stress granule, Cell Line, Tumor, medicine, Humans, HELICASE, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], STRESS GRANULES, Helicase, RNA, Correction, medicine.disease, GENE, 030104 developmental biology, HEK293 Cells, biology.protein, 030217 neurology & neurosurgery, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: Contains fulltext : 182457.pdf (Publisher’s version ) (Open Access) DHX30 is a member of the family of DExH-box helicases, which use ATP hydrolysis to unwind RNA secondary structures. Here we identified six different de novo missense mutations in DHX30 in twelve unrelated individuals affected by global developmental delay (GDD), intellectual disability (ID), severe speech impairment and gait abnormalities. While four mutations are recurrent, two are unique with one affecting the codon of one recurrent mutation. All amino acid changes are located within highly conserved helicase motifs and were found to either impair ATPase activity or RNA recognition in different in vitro assays. Moreover, protein variants exhibit an increased propensity to trigger stress granule (SG) formation resulting in global translation inhibition. Thus, our findings highlight the prominent role of translation control in development and function of the central nervous system and also provide molecular insight into how DHX30 dysfunction might cause a neurodevelopmental disorder.
Published: 2017
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37. 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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38. Genetic epilepsy with febrile seizures plus

Author: Samuel F. Berkovic, Andrew Bleasel, Hadassa Goldberg-Stern, Bronwyn E. Grinton, Sara Kivity, Leanne M. Dibbens, Elizabeth K. Ruzzo, John A. Damiano, Lata Vadlamudi, Zaid Afawi, Georgie C. Glubb, Jodie P. Malone, Rosemary Burgess, Padraic Grattan-Smith, Yue-Hua Zhang, Danya F. Vears, Katherine L. Helbig, Amos D. Korczyn, Ingrid E. Scheffer, Susannah T. Bellows, and Michael S. Hildebrand
Subjects: Adult, Male, 0301 basic medicine, Adolescent, Seizures, Febrile, Genetic epilepsy, Young Adult, 03 medical and health sciences, Epilepsy, 0302 clinical medicine, Childhood absence epilepsy, medicine, Humans, Age of Onset, Focal Epilepsies, Generalized epilepsy, Child, business.industry, Infant, Genetic data, Middle Aged, medicine.disease, Pedigree, Phenotype, 030104 developmental biology, Child, Preschool, Immunology, Epilepsy, Generalized, Female, Epilepsies, Partial, Neurology (clinical), Age of onset, business, Generalized epilepsy with febrile seizures plus, 030217 neurology & neurosurgery
Abstract: Objective:Following our original description of generalized epilepsy with febrile seizures plus (GEFS+) in 1997, we analyze the phenotypic spectrum in 409 affected individuals in 60 families (31 new families) and expand the GEFS+ spectrum.Methods:We performed detailed electroclinical phenotyping on all available affected family members. Genetic analysis of known GEFS+ genes was carried out where possible. We compared our phenotypic and genetic data to those published in the literature over the last 19 years.Results:We identified new phenotypes within the GEFS+ spectrum: focal seizures without preceding febrile seizures (16/409 [4%]), classic genetic generalized epilepsies (22/409 [5%]), and afebrile generalized tonic-clonic seizures (9/409 [2%]). Febrile seizures remains the most frequent phenotype in GEFS+ (178/409 [44%]), followed by febrile seizures plus (111/409 [27%]). One third (50/163 [31%]) of GEFS+ families tested have a pathogenic variant in a known GEFS+ gene.Conclusion:As 37/409 (9%) affected individuals have focal epilepsies, we suggest that GEFS+ be renamed genetic epilepsy with febrile seizures plus rather than generalized epilepsy with febrile seizures plus. The phenotypic overlap between GEFS+ and the classic generalized epilepsies is considerably greater than first thought. The clinical and molecular data suggest that the 2 major groups of generalized epilepsies share genetic determinants.
Published: 2017
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39. The role of genetic testing in epilepsy diagnosis and management

Author: Yvonne G. Weber, Holger Lerche, Saskia Biskup, Sarah von Spiczak, and Katherine L. Helbig
Subjects: 0301 basic medicine, Genetic counseling, Neurological disorder, Bioinformatics, Pathology and Forensic Medicine, 03 medical and health sciences, Epilepsy, 0302 clinical medicine, Genetic variation, Genetics, medicine, Humans, Genetic Testing, Molecular Biology, Exome, Genetic testing, medicine.diagnostic_test, business.industry, medicine.disease, Precision medicine, 030104 developmental biology, Molecular Medicine, Personalized medicine, business, 030217 neurology & neurosurgery
Abstract: Epilepsy is a common neurological disorder characterized by recurrent unprovoked seizures. More than 500 epilepsy-associated genes have been described in the literature. Most of these genes play an important role in neuronal excitability, cortical development or synaptic transmission. A growing number of genetic variations have implications on diagnosis and prognostic or therapeutic advice in terms of a personalized medicine. Area covered: The review presents the different forms of genetic epilepsies with respect to their underlying genetic and functional pathophysiology and aims to give advice for recommended genetic testing. Moreover, it discusses ethical and legal guidelines, costs and technical limitations which should be considered. Expert commentary: Genetic testing is an important component in the diagnosis and treatment of many forms of epilepsy.
Published: 2017
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40. GRIN2Bencephalopathy: novel findings on phenotype, variant clustering, functional consequences and treatment aspects

Author: Arndt Rolfs, Douglas R. Smith, Hongjie Yuan, Markus Wolff, Eirik Frengen, Sarah E Parisotto, Mark A. Tarnopolsky, John Millichap, Katherine L. Helbig, Christian Korff, Lutz Dondit, Anna-Elina Lehesjoki, Alison M. Muir, Brad T. Tinkle, Heather C Mefford, Bodo Laube, Anne T. Berg, Wen-Hann Tan, Kelly L. Jones, Floor E. Jansen, Christine M. Stanley, Candace T. Myers, Isabelle De Bie, John A. Lawson, Henrike O. Heyne, Wenjuan Chen, David Neal Franz, Julie R. Jones, Elysa J. Marco, Nataliya Di Donato, Cyril Mignot, Jasper J. van der Smagt, Stephen F. Traynelis, Tarja Linnankivi, Tim M. Strom, Hirofumi Kusumoto, Rena Vanzo, Petter Strømme, Uffe Birk Jensen, Amy Lacroix, Darius J Adams, Chun Hu, Boris Keren, Sha Tang, Richard J. Leventer, Johannes R. Lemke, Levinus A. Bok, Helio Pedro, Rami Abou Jamra, Dianalee McKnight, Ethan M. Goldberg, Tony Roscioli, Lauren Brady, Konrad Platzer, Philippe Major, Amy Decker, Anup D. Patel, Marcia C. Willing, Ingrid E. Scheffer, Mark Mintz, Eva H. Brilstra, Carolina Courage, Lynette G. Sadleir, Alexander Winschel, William B. Dobyns, Stephanie Fox, Emmanuelle Ranza, Saskia Biskup, Dennis Döcker, Judith D. Ranells, Rikke S. Møller, Elaine H. Zackai, Hannah Schütz, Mieke M. van Haelst, Christel Depienne, Medicum, Research Programme for Molecular Neurology, Department of Medical and Clinical Genetics, Research Programs Unit, Neuroscience Center, Anna-Elina Lehesjoki / Principal Investigator, University of Helsinki, Children's Hospital, Clinicum, Lastenneurologian yksikkö, HUS Children and Adolescents, Amsterdam Reproduction & Development (AR&D), Human genetics, and Amsterdam Neuroscience - Complex Trait Genetics
Subjects: 0301 basic medicine, INTELLECTUAL DISABILITY, Brain Diseases/drug therapy/genetics, Pathogenic GRIN2B mutations, AUTISM SPECTRUM DISORDERS, Cortical visual impairment, Bioinformatics, Clustering of missense variants, 3124 Neurology and psychiatry, Epilepsy, 0302 clinical medicine, Channelopathy, NMDA RECEPTORS, Receptors, Intellectual disability, Polymicrogyria, Genetics(clinical), Molecular Targeted Therapy, Genetics (clinical), ddc:618, biology, Epileptic encephalopathy, Precision medicine, 1184 Genetics, developmental biology, physiology, Magnetic Resonance Imaging, Memantine/therapeutic use, Hypotonia, 3. Good health, N-Methyl-D-Aspartate/antagonists & inhibitors/genetics/metabolism, Phenotype, medicine.symptom, Heterozygote, GENES, Mutation/genetics, MIGRATION, Clustering Of Missense Variants, Epileptic Encephalopathy, Pathogenic Grin2b Mutations, Precision Medicine, Encephalopathy, Neuroimaging, Article, 03 medical and health sciences, Journal Article, Genetics, medicine, Humans, NEURODEVELOPMENTAL DISORDERS, business.industry, 3112 Neurosciences, medicine.disease, INDIVIDUALS, 030104 developmental biology, DE-NOVO MUTATIONS, FOCAL EPILEPSY, SUBUNIT, biology.protein, Autism, GRIN2B, 3111 Biomedicine, business, 030217 neurology & neurosurgery
Abstract: BACKGROUND: We aimed for a comprehensive delineation of genetic, functional and phenotypic aspects of GRIN2B encephalopathy and explored potential prospects of personalised medicine.METHODS: Data of 48 individuals with de novo GRIN2B variants were collected from several diagnostic and research cohorts, as well as from 43 patients from the literature. Functional consequences and response to memantine treatment were investigated in vitro and eventually translated into patient care.RESULTS: Overall, de novo variants in 86 patients were classified as pathogenic/likely pathogenic. Patients presented with neurodevelopmental disorders and a spectrum of hypotonia, movement disorder, cortical visual impairment, cerebral volume loss and epilepsy. Six patients presented with a consistent malformation of cortical development (MCD) intermediate between tubulinopathies and polymicrogyria. Missense variants cluster in transmembrane segments and ligand-binding sites. Functional consequences of variants were diverse, revealing various potential gain-of-function and loss-of-function mechanisms and a retained sensitivity to the use-dependent blocker memantine. However, an objectifiable beneficial treatment response in the respective patients still remains to be demonstrated.CONCLUSIONS: In addition to previously known features of intellectual disability, epilepsy and autism, we found evidence that GRIN2B encephalopathy is also frequently associated with movement disorder, cortical visual impairment and MCD revealing novel phenotypic consequences of channelopathies.
Published: 2017
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41. Biallelic loss-of-function variants inDOCK3cause muscle hypotonia, ataxia, and intellectual disability

Author: Milen Velinov, Cameron Mroske, Katherine L. Helbig, Divya Moorthy, and Samin A. Sajan
Subjects: 0301 basic medicine, Proband, Genetics, Muscle Hypotonia, Ataxia, Biology, Hypotonia, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, Chromosomal region, medicine, Gait Ataxia, medicine.symptom, Ataxic Gait, 030217 neurology & neurosurgery, Genetics (clinical), Exome sequencing
Abstract: DOCK3 encodes the dedicator of cytokinesis 3 protein, a member of the DOCK180 family of proteins that are characterized by guanine nucleotide exchange factor activity. DOCK3 is expressed exclusively in the central nervous system and plays an important role in axonal outgrowth and cytoskeleton reorganization. Dock3 knockout mice exhibit motor deficiencies with abnormal ataxic gait and impaired learning. We report two siblings with biallelic loss-of-function variants in DOCK3. Diagnostic whole exome sequencing and chromosomal microarray were performed on a proband with severe intellectual disability, hypotonia, and ataxic gait. Testing was also performed on the proband's similarly affected brother. A paternally inherited 458 kb deletion in chromosomal region 3p21.2 disrupting the DOCK3 gene was identified in both affected siblings. Whole exome sequencing identified a nonsense variant c.382C>G (p.Gln128*) in the DOCK3 gene (NM_004947) on the maternal allele in both siblings. Common features in both affected individuals include severe intellectual disability, ataxic gait, and severe hypotonia, which recapitulates the Dock3 knockout mouse phenotype. We demonstrate that complete DOCK3 deficiency in humans leads to intellectual disability with significant hypotonia and gait ataxia, likely due to abnormal axonal development.
Published: 2017
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42. Classification of Genes: Standardized Clinical Validity Assessment of Gene–Disease Associations Aids Diagnostic Exome Analysis and Reclassifications

Author: Kendra Waller, Deepali N. Shinde, Mari Rossi, Zöe Powis, Kelly Radtke, Erica D. Smith, Sourat Darabi, Sha Tang, Kelly D. Farwell Hagman, Katherine L. Helbig, Dima El-Khechen, and Dorothy K. Grange
Subjects: 0301 basic medicine, medicine.medical_specialty, Scoring system, Context (language use), Disease, Biology, Bioinformatics, reclassifications, gene–disease association, 03 medical and health sciences, Acquired immunodeficiency syndrome (AIDS), clinical validity, Genetics, medicine, Methods, Humans, Exome, SCYL1, Intensive care medicine, novel candidate genetic etiology, Genetics (clinical), Exome sequencing, Genetic Association Studies, Clinical genomics, High-Throughput Nucleotide Sequencing, Reproducibility of Results, Genomics, Sequence Analysis, DNA, medicine.disease, diagnostic exome sequencing, 030104 developmental biology, SNAP25, characterized genetic etiology, Clinical validity
Abstract: Ascertaining a diagnosis through exome sequencing can provide potential benefits to patients, insurance companies, and the healthcare system. Yet, as diagnostic sequencing is increasingly employed, vast amounts of human genetic data are produced that need careful curation. We discuss methods for accurately assessing the clinical validity of gene–disease relationships to interpret new research findings in a clinical context and increase the diagnostic rate. The specifics of a gene–disease scoring system adapted for use in a clinical laboratory are described. In turn, clinical validity scoring of gene–disease relationships can inform exome reporting for the identification of new or the upgrade of previous, clinically relevant gene findings. Our retrospective analysis of all reclassification reports from the first 4 years of diagnostic exome sequencing showed that 78% were due to new gene–disease discoveries published in the literature. Among all exome positive/likely positive findings in characterized genes, 32% were in genetic etiologies that were discovered after 2010. Our data underscore the importance and benefits of active and up‐to‐date curation of a gene–disease database combined with critical clinical validity scoring and proactive reanalysis in the clinical genomics era.
Published: 2017

43. Candidate-gene criteria for clinical reporting: diagnostic exome sequencing identifies altered candidate genes among 8% of patients with undiagnosed diseases

Author: Deepali N. Shinde, Elizabeth C. Chao, Kelly Radtke, Sitao Wu, Zöe Powis, Mari Rossi, Shuwei Li, Katherine L. Helbig, Samin A. Sajan, Cameron Mroske, Hsiao-Mei Lu, Mark E. Nunes, Kelly D. Farwell Hagman, Sha Tang, Wendy Alcaraz, Dima El-Khechen, Layla Shahmirzadi, Robert Huether, and Erica D. Smith
Subjects: 0301 basic medicine, Genetics, 03 medical and health sciences, Candidate gene, 030104 developmental biology, business.industry, Mutation (genetic algorithm), Medicine, business, Exome, Genetics (clinical), Exome sequencing
Abstract: Candidate-gene criteria for clinical reporting: diagnostic exome sequencing identifies altered candidate genes among 8% of patients with undiagnosed diseases
Published: 2017
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44. Correction: A longitudinal footprint of genetic epilepsies using automated electronic medical record interpretation

Author: Shiva Ganesan, Peter D. Galer, Pouya Khankhanian, Margaret O'Brien, Alex Felmeister, Colin A Ellis, Sarah E McKeown, Ingo Helbig, Alexander K. Gonzalez, and Katherine L. Helbig
Subjects: Epilepsy, business.industry, Correction, Neurogenetics, Disease, medicine.disease, Clinical decision support system, Epileptic spasms, Phenotype, Intellectual Disability, Intellectual disability, Human Phenotype Ontology, Etiology, medicine, Electronic Health Records, Humans, Medical diagnosis, Child, business, Spasms, Infantile, Genetics (clinical), Clinical psychology
Abstract: PURPOSE Childhood epilepsies have a strong genetic contribution, but the disease trajectory for many genetic etiologies remains unknown. Electronic medical record (EMR) data potentially allow for the analysis of longitudinal clinical information but this has not yet been explored. METHODS We analyzed provider-entered neurological diagnoses made at 62,104 patient encounters from 658 individuals with known or presumed genetic epilepsies. To harmonize clinical terminology, we mapped clinical descriptors to Human Phenotype Ontology (HPO) terms and inferred higher-level phenotypic concepts. We then binned the resulting 286,085 HPO terms to 100 3-month time intervals and assessed gene-phenotype associations at each interval. RESULTS We analyzed a median follow-up of 6.9 years per patient and a cumulative 3251 patient years. Correcting for multiple testing, we identified significant associations between "Status epilepticus" with SCN1A at 1.0 years, "Severe intellectual disability" with PURA at 9.75 years, and "Infantile spasms" and "Epileptic spasms" with STXBP1 at 0.5 years. The identified associations reflect known clinical features of these conditions, and manual chart review excluded provider bias. CONCLUSION Some aspects of the longitudinal disease histories can be reconstructed through EMR data and reveal significant gene-phenotype associations, even within closely related conditions. Gene-specific EMR footprints may enable outcome studies and clinical decision support.
Published: 2020
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45. Correction: IQSEC2-related encephalopathy in males and females:a comparative study including 37 novel patients

Author: Petra Laššuthová, Kathryn G. Miller, Jacques L. Michaud, Sarah Weckhuysen, Claude Besmond, Stéphanie Gobin-Limballe, Emílie Vyhnálková, Aoife McMahon, Peter M. van Hasselt, Christine Barnerias, Laurence Hubert, Joannella Morales, Daphné Lehalle, Caroline Lacoste, Rima Nabbout, Hubert Journel, Jasper J. van der Smagt, Patrick Edery, Marjan J. A. van Kempen, Samuel P. Yang, Fiona Cunningham, Thomas Smol, Delphine Héron, Darina Prchalova, David Geneviève, Thierry Bienvenu, Mathieu Milh, Bénédicte Duban-Bedu, Ledia Brunga, Marleen Simon, Ana G. Cristancho, Ethan M. Goldberg, Sandra Janssens, Christel Depienne, Miroslava Hancarova, Shoji Ichikawa, Berge A. Minassian, Ivan Shelihan, Elsa Rossignol, Ange Line Bruel, Elena Gardella, Marije Koopmans, Arnold Munnich, Natasha Shur, Pauline Marzin, Ingo Helbig, Julien Buratti, Alyssa R. Rosen, Giulia Barcia, Claire Davidson, Berten Ceulemans, Marilyn Tallot, Marie Line Jacquemont, Guillaume Smits, Catheline Vilain, Katherine L. Helbig, Gaetan Lesca, Rikke S. Møller, Claire Bar, Marie Laure Moutard, Caroline Nava, Marie Bertille Dehouck, Julie Soblet, Philippe M. Campeau, Cyril Mignot, Laurent Villard, Joelle Roume, Julia Metreau, Dragan Marjanovic, Damien Lederer, Audrey Putoux, Chloé Quélin, Fadi F. Hamdan, Boris Keren, Anna Kaminska, Xilma R. Ortiz-Gonzalez, Christine Ioos, Christine Coubes, Julie Gauthier, Nienke E. Verbeek, Bobby P. C. Koeleman, Eveline Hagebeuk, Jean Marc Pinard, Katalin Štěrbová, Christèle Dubourg, and Elizabeth J. Donner
Subjects: Pediatrics, medicine.medical_specialty, Text mining, business.industry, Published Erratum, Encephalopathy, Medizin, MEDLINE, Medicine, business, medicine.disease, Genetics (clinical)
Abstract: This Article was originally published under Nature Research’s License to Publish, but has now been made available under a CC BY 4.0 license. The PDF and HTML versions of the Article have been modified accordingly.
Published: 2019
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46. Heterozygous Variants in KMT2E Cause a Spectrum of Neurodevelopmental Disorders and Epilepsy

Author: Anne H. O’Donnell-Luria, Lynn S. Pais, Víctor Faundes, Jordan C. Wood, Abigail Sveden, Victor Luria, Rami Abou Jamra, Andrea Accogli, Kimberly Amburgey, Britt Marie Anderlid, Silvia Azzarello-Burri, Alice A. Basinger, Claudia Bianchini, Lynne M. Bird, Rebecca Buchert, Wilfrid Carre, Sophia Ceulemans, Perrine Charles, Helen Cox, Lisa Culliton, Aurora Currò, Florence Demurger, James J. Dowling, Benedicte Duban-Bedu, Christèle Dubourg, Saga Elise Eiset, Luis F. Escobar, Alessandra Ferrarini, Tobias B. Haack, Mona Hashim, Solveig Heide, Katherine L. Helbig, Ingo Helbig, Raul Heredia, Delphine Héron, Bertrand Isidor, Amy R. Jonasson, Pascal Joset, Boris Keren, Fernando Kok, Hester Y. Kroes, Alinoë Lavillaureix, Xin Lu, Saskia M. Maas, Gustavo H.B. Maegawa, Carlo L.M. Marcelis, Paul R. Mark, Marcelo R. Masruha, Heather M. McLaughlin, Kirsty McWalter, Esther U. Melchinger, Saadet Mercimek-Andrews, Caroline Nava, Manuela Pendziwiat, Richard Person, Gian Paolo Ramelli, Luiza L.P. Ramos, Anita Rauch, Caitlin Reavey, Alessandra Renieri, Angelika Rieß, Amarilis Sanchez-Valle, Shifteh Sattar, Carol Saunders, Niklas Schwarz, Thomas Smol, Myriam Srour, Katharina Steindl, Steffen Syrbe, Jenny C. Taylor, Aida Telegrafi, Isabelle Thiffault, Doris A. Trauner, Helio van der Linden, Silvana van Koningsbruggen, Laurent Villard, Ida Vogel, Julie Vogt, Yvonne G. Weber, Ingrid M. Wentzensen, Elysa Widjaja, Jaroslav Zak, Samantha Baxter, Siddharth Banka, Lance H. Rodan, Jeremy F. McRae, Stephen Clayton, Tomas W. Fitzgerald, Joanna Kaplanis, Elena Prigmore, Diana Rajan, Alejandro Sifrim, Stuart Aitken, Nadia Akawi, Mohsan Alvi, Kirsty Ambridge, Daniel M. Barrett, Tanya Bayzetinova, Philip Jones, Wendy D. Jones, Daniel King, Netravathi Krishnappa, Laura E. Mason, Tarjinder Singh, Adrian R. Tivey, Munaza Ahmed, Uruj Anjum, Hayley Archer, Ruth Armstrong, Jana Awada, Meena Balasubramanian, Diana Baralle, Angela Barnicoat, Paul Batstone, David Baty, Chris Bennett, Jonathan Berg, Birgitta Bernhard, A. Paul Bevan, Maria Bitner-Glindzicz, Edward Blair, Moira Blyth, David Bohanna, Louise Bourdon, David Bourn, Lisa Bradley, Angela Brady, Simon Brent, Carole Brewer, Kate Brunstrom, David J. Bunyan, John Burn, Natalie Canham, Bruce Castle, Kate Chandler, Elena Chatzimichali, Deirdre Cilliers, Angus Clarke, Susan Clasper, Jill Clayton-Smith, Virginia Clowes, Andrea Coates, Trevor Cole, Irina Colgiu, Amanda Collins, Morag N. Collinson, Fiona Connell, Nicola Cooper, Lara Cresswell, Gareth Cross, Yanick Crow, Mariella D’Alessandro, Tabib Dabir, Rosemarie Davidson, Sally Davies, Dylan de Vries, John Dean, Charu Deshpande, Gemma Devlin, Abhijit Dixit, Angus Dobbie, Alan Donaldson, Dian Donnai, Deirdre Donnelly, Carina Donnelly, Angela Douglas, Sofia Douzgou, Alexis Duncan, Jacqueline Eason, Sian Ellard, Ian Ellis, Frances Elmslie, Karenza Evans, Sarah Everest, Tina Fendick, Richard Fisher, Frances Flinter, Nicola Foulds, Andrew Fry, Alan Fryer, Carol Gardiner, Lorraine Gaunt, Neeti Ghali, Richard Gibbons, Harinder Gill, Judith Goodship, David Goudie, Emma Gray, Andrew Green, Philip Greene, Lynn Greenhalgh, Susan Gribble, Rachel Harrison, Lucy Harrison, Victoria Harrison, Rose Hawkins, Liu He, Stephen Hellens, Alex Henderson, Sarah Hewitt, Lucy Hildyard, Emma Hobson, Simon Holden, Muriel Holder, Susan Holder, Georgina Hollingsworth, Tessa Homfray, Mervyn Humphreys, Jane Hurst, Ben Hutton, Stuart Ingram, Melita Irving, Lily Islam, Andrew Jackson, Joanna Jarvis, Lucy Jenkins, Diana Johnson, Elizabeth Jones, Dragana Josifova, Shelagh Joss, Beckie Kaemba, Sandra Kazembe, Rosemary Kelsell, Bronwyn Kerr, Helen Kingston, Usha Kini, Esther Kinning, Gail Kirby, Claire Kirk, Emma Kivuva, Alison Kraus, Dhavendra Kumar, V. K. Ajith Kumar, Katherine Lachlan, Wayne Lam, Anne Lampe, Caroline Langman, Melissa Lees, Derek Lim, Cheryl Longman, Gordon Lowther, Sally A. Lynch, Alex Magee, Eddy Maher, Alison Male, Sahar Mansour, Karen Marks, Katherine Martin, Una Maye, Emma McCann, Vivienne McConnell, Meriel McEntagart, Ruth McGowan, Kirsten McKay, Shane McKee, Dominic J. McMullan, Susan McNerlan, Catherine McWilliam, Sarju Mehta, Kay Metcalfe, Anna Middleton, Zosia Miedzybrodzka, Emma Miles, Shehla Mohammed, Tara Montgomery, David Moore, Sian Morgan, Jenny Morton, Hood Mugalaasi, Victoria Murday, Helen Murphy, Swati Naik, Andrea Nemeth, Louise Nevitt, Ruth Newbury-Ecob, Andrew Norman, Rosie O’Shea, Caroline Ogilvie, Kai-Ren Ong, Soo-Mi Park, Michael J. Parker, Chirag Patel, Joan Paterson, Stewart Payne, Daniel Perrett, Julie Phipps, Daniela T. Pilz, Martin Pollard, Caroline Pottinger, Joanna Poulton, Norman Pratt, Katrina Prescott, Sue Price, Abigail Pridham, Annie Procter, Hellen Purnell, Oliver Quarrell, Nicola Ragge, Raheleh Rahbari, Josh Randall, Julia Rankin, Lucy Raymond, Debbie Rice, Leema Robert, Eileen Roberts, Jonathan Roberts, Paul Roberts, Gillian Roberts, Alison Ross, Elisabeth Rosser, Anand Saggar, Shalaka Samant, Julian Sampson, Richard Sandford, Ajoy Sarkar, Susann Schweiger, Richard Scott, Ingrid Scurr, Ann Selby, Anneke Seller, Cheryl Sequeira, Nora Shannon, Saba Sharif, Charles Shaw-Smith, Emma Shearing, Debbie Shears, Eamonn Sheridan, Ingrid Simonic, Roldan Singzon, Zara Skitt, Audrey Smith, Kath Smith, Sarah Smithson, Linda Sneddon, Miranda Splitt, Miranda Squires, Fiona Stewart, Helen Stewart, Volker Straub, Mohnish Suri, Vivienne Sutton, Ganesh Jawahar Swaminathan, Elizabeth Sweeney, Kate Tatton-Brown, Cat Taylor, Rohan Taylor, Mark Tein, I. Karen Temple, Jenny Thomson, Marc Tischkowitz, Susan Tomkins, Audrey Torokwa, Becky Treacy, Claire Turner, Peter Turnpenny, Carolyn Tysoe, Anthony Vandersteen, Vinod Varghese, Pradeep Vasudevan, Parthiban Vijayarangakannan, Emma Wakeling, Sarah Wallwark, Jonathon Waters, Astrid Weber, Diana Wellesley, Margo Whiteford, Sara Widaa, Sarah Wilcox, Emily Wilkinson, Denise Williams, Nicola Williams, Louise Wilson, Geoff Woods, Christopher Wragg, Michael Wright, Laura Yates, Michael Yau, Chris Nellåker, Michael Parker, Helen V. Firth, Caroline F. Wright, David R. FitzPatrick, Jeffrey C. Barrett, Matthew E. Hurles, Department of Medicine 1, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Center for Medical Genetics, Istituto di Scienze e Tecnologie della Cognizione, Consiglio Nazionale delle Ricerche (ISTC, CNR), Istituto di Scienze e Tecnologie della Cognizione, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Génétique médicale [Centre Hospitalier de Vannes], Centre hospitalier Bretagne Atlantique (Morbihan) (CHBA), Department of Pediatrics, University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, Centre de Génétique Chromosomique [Hôpital Saint Vincent de Paul], Hôpital Saint Vincent de Paul-Groupement des Hôpitaux de l'Institut Catholique de Lille (GHICL), Université catholique de Lille (UCL)-Université catholique de Lille (UCL), Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Service de génétique médicale, Centre Hospitalier Universitaire Vaudois [Lausanne] (CHUV), Institute of Human Genetics, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM)-Helmholtz Zentrum München = German Research Center for Environmental Health, Groupe de Recherche Clinique : Déficience Intellectuelle et Autisme (GRC), Université Pierre et Marie Curie - Paris 6 (UPMC), Children’s Hospital of Philadelphia (CHOP ), Service de Génétique Médicale, Centre hospitalier universitaire de Nantes (CHU Nantes), Department of Public Health Sciences, Karolinska Institutet [Stockholm], Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Baylor University-Baylor University, Institute of Medical Genetics, Universität Zürich [Zürich] = University of Zurich (UZH), Università degli Studi di Camerino = University of Camerino (UNICAM), Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), University of Oxford, GeneDx [Gaithersburg, MD, USA], Department of Clinical Genetics (Academic Medical Center, University of Amsterdam), VU University Medical Center [Amsterdam], Marseille medical genetics - Centre de génétique médicale de Marseille (MMG), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Clinical Genetics, Aarhus University Hospital, Boston Children's Hospital, Wellcome Trust Genome Campus, The Wellcome Trust Sanger Institute [Cambridge], Institute of Biomedical Engineering [Oxford] (IBME), Climatic Research Unit, University of East Anglia [Norwich] (UEA), Imperial College London, St Mary's Hospital, East Anglian Medical Genetics Service, Cytogenetics Laboratory, Addenbrooke's Hospital, Sheffield Children's NHS Foundation Trust, Regional Genetic Service, St Mary's Hospital, Manchester, Genetics, University of Southampton, Great Ormond Street Hospital for Children [London] (GOSH), Yorkshire Regional Clinical Genetics Service, Chapel Allerton Hospital, Molecular and Clinical Medicine [Dundee, UK] (School of Medicine), University of Dundee [UK]-Ninewells Hospital & Medical School [Dundee, UK], Department of Clinical Genetics, Oxford Regional Genetics Service, The Churchill hospital, North West Thames Regional Genetics, Northwick Park Hospital, Royal Devon & Exeter Hospital, Wessex Clinical Genetics Service, Wessex clinical genetics service, Manchester University NHS Foundation Trust (MFT), West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Our Lady's hospital for Sick Children, Our Lady's Hospital for Sick Children, Guy's Hospital [London], University Hospitals Leicester, University of Edinburgh, Belfast City Hospital, Ferguson-Smith Centre for Clinical Genetics, Yorkhill Hospitals, Institute of Medical Genetics, Heath Park, Cardiff, The London Clinic, Nottingham City Hospital, Clinical Genetics Department, St Michael's Hospital, Department of Genetic Medicine, Nottingham Clinical Genetics Service, Nottingham University Hospitals NHS Trust (NUH), Royal Devon and Exeter Foundation Trust, Histopathology, St. George's Hospital, Teesside Genetics Unit, James Cook University (JCU), Kansas State University, Liverpool Women's NHS Foundation Trust, Department of Medical Genetics, HMNC Brain Health, North West Thames Regional Genetics Service, Northwick Park Hospital, Harrow, Leicester Royal Infirmary, University Hospitals Leicester-University Hospitals Leicester, Ninewells Hospital and Medical School [Dundee], Academic Centre on Rare Diseases (ACoRD), University College Dublin [Dublin] (UCD), Oxford Brookes University, Institute of medicinal plant development, Chinese Academy of Medical Sciences, Newcastle Upon Tyne Hospitals NHS Trust, Service d'explorations fonctionnelles respiratoires [Lille], Department of Computer Science - Trinity College Dublin, University of Dublin, Department of Clinical Genetics (Sheffield Children’s NHS Foundation Trust), Division of Medical & Molecular Genetics, NHS Greater Glasgow & Clyde [Glasgow] (NHSGGC), Department of Clinical Genetics [Churchill Hospital], Churchill Hospital Oxford Centre for Haematology, Weizmann Institute of Science [Rehovot, Israël], Southampton General Hospital, Western General Hospital, Head of the Department of Medical Genetics, University of Birmingham [Birmingham], SW Thames Regional Genetics Service, St Georgeâ™s University of London, London, Institut Cochin (IC UM3 (UMR 8104 / U1016)), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), All Wales Medical Genetics Services, Singleton Hospital, Central Manchester University Hospitals NHS Foundation Trust, University of North Texas (UNT), Clinical Genetics, Northern Genetics Service, Newcastle University [Newcastle], United Kingdom Met Office [Exeter], Institute of Medical Genetics (University Hospital of Wales), University Hospital of Wales (UHW), West Midlands Regional Genetics Laboratory and Clinical Genetics Unit, Birmingham Women's Hospital, Laboratory of Molecular Genetics, National Institute of Child Health and Human Development, National Institutes of Health, Department of Genetics, Cell- and Immunobiology, Semmelweis University, University Hospitals Bristol, Marketing (MKT), EESC-GEM Grenoble Ecole de Management, Addenbrookes Hospital, West of Scotland Genetics Service (Queen Elizabeth University Hospital), University Hospital Birmingham Queen Elizabeth, Department of Clnical Genetics, Chapel Allerton Hospital, Department of Clinical Genetics, Northampton General Hospital, Northampton, Royal Devon and Exeter Hospital [Exeter, UK] (RDEH), Guy's and St Thomas' Hospital [London], School of Computer Science, Bangor University, University Hospital Southampton, Clinical Genetics Unit, St Georges, University of London, Medical Genetics, Cardiff University, Research and Development, Futurelab, Nottingham Regional Genetics Service [Nottingham, UK], Nottingham University Hospitals NHS Trust (NUH)-City Hospital Campus [Nottingham, UK], University of St Andrews [Scotland], Clinical Genetics Service, Nottingham University Hospitals NHS Trust - City Hospital Campus, West Midlands Regional Genetics Unit, Department of Neurology, Johns Hopkins University (JHU), Oxford University Hospitals NHS Trust, St James's University Hospital, Leeds Teaching Hospitals NHS Trust, Addenbrooke's Hospital, Cambridge University NHS Trust, Institute of Human Genetics, Newcastle, Division of Biological Stress Response [Amsterdam, The Netherlands], The Netherlands Cancer Institute [Amsterdam, The Netherlands], Johns Hopkins Bloomberg School of Public Health [Baltimore], Birmingham Women’s Hospital, Department of Genetics, Portuguese Oncology Institute, Molecular Genetics, IWK Health Centre, IWK health centre, North West london hospitals NHS Trust, Department of Clinical Genetics (Queen Elizabeth University Hospital, Glasgow), Queen Elizabeth University Hospital (Glasgow), Birmingham women's hospital, Birmingham, Ethox Centre, Department of Public Health and Primary Health Care, University of Oxford, Badenoch Building, Old Road Campus, Headington, R01 HD091846, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Human Genome Research Institute, National Institutes of Health’s National Institute of Child Health and Human Development, Boston Children’s Hospital Faculty Development Fellowship, UM1HG008900, Broad Center for Mendelian Genomics, Chile’s National Commission for Scientific and Technological Research, DFG WE4896/3-1, German Research Society, WT 100127, Health Innovation Challenge Fund, Comprehensive Clinical Research Network, Skaggs-Oxford Scholarship, 10/H0305/83, Cambridge South REC, REC GEN/284/12, Republic of Ireland, WT098051, Wellcome Sanger Institute, 72160007, Comisión Nacional de Investigación Científica y Tecnológica, Children's Hospital of Philadelphia, Technische Universität Kaiserslautern, 1DH1813319, Dietmar Hopp Stiftung, National Institute for Health Research, Department of Health & Social Care, Service de neurologie 1 [CHU Pitié-Salpétrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Hôpital Saint Vincent de Paul-GHICL, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM)-Helmholtz-Zentrum München (HZM)-German Research Center for Environmental Health, Service de Génétique Cytogénétique et Embryologie [CHU Pitié-Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Università degli Studi di Camerino (UNICAM), University of Oxford [Oxford], Institut National de la Santé et de la Recherche Médicale (INSERM)-Aix Marseille Université (AMU), Nottingham University Hospitals NHS Trust, Nottingham University Hospitals, SW Thames Regional Genetics Service, St Georgeâ™s University of London, London, University Hospital of Wales, Grenoble Ecole de Management, Royal Devon and Exeter Hospital, City Hospital Campus [Nottingham, UK]-Nottingham University Hospitals NHS Trust [UK], ANS - Complex Trait Genetics, Human Genetics, ARD - Amsterdam Reproduction and Development, ACS - Pulmonary hypertension & thrombosis, Service de Neurologie [CHU Pitié-Salpêtrière], IFR70-CHU Pitié-Salpêtrière [AP-HP], GHICL-Hôpital Saint Vincent de Paul, Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Friedrich-Alexander d'Erlangen-Nuremberg, Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Pitié-Salpêtrière [APHP], Centre Hospitalier Bretagne Atlantique [Vannes], Technische Universität München [München] (TUM)-Helmholtz-Zentrum München (HZM)-German Research Center for Environmental Health, Service de Génétique et Cytogénétique [CHU Pitié-Salpêtrière], University of Zürich [Zürich] (UZH), Università di Camerino (UNICAM), Birmingham Women's Hospital Healthcare NHS Trust, University Hospitals of Leicester, Sheffield Children’s Hospital, Weizmann Institute of Science, and Grenoble Ecole de Management (GEM)
Subjects: 0301 basic medicine, Male, Microcephaly, [SDV]Life Sciences [q-bio], Haploinsufficiency, autism, epilepsy, epileptic encephalopathy, global developmental delay, H3K4 methylation, intellectual disability, KMT2E, neurodevelopmental disorder, Adolescent, Adult, Child, Child, Preschool, DNA-Binding Proteins, Epilepsy, Female, Humans, Infant, Neurodevelopmental Disorders, Pedigree, Phenotype, Young Adult, Genetic Variation, Heterozygote, 0302 clinical medicine, Neurodevelopmental disorder, Intellectual disability, Global developmental delay, Genetics (clinical), ComputingMilieux_MISCELLANEOUS, Genetics, 0303 health sciences, Hypotonia, 030220 oncology & carcinogenesis, medicine.symptom, Rare cancers Radboud Institute for Health Sciences [Radboudumc 9], 03 medical and health sciences, Report, medicine, Journal Article, Expressivity (genetics), Preschool, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, business.industry, Macrocephaly, medicine.disease, 030104 developmental biology, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Autism, business, 030217 neurology & neurosurgery
Abstract: Contains fulltext : 206572.pdf (Publisher’s version ) (Open Access) We delineate a KMT2E-related neurodevelopmental disorder on the basis of 38 individuals in 36 families. This study includes 31 distinct heterozygous variants in KMT2E (28 ascertained from Matchmaker Exchange and three previously reported), and four individuals with chromosome 7q22.2-22.23 microdeletions encompassing KMT2E (one previously reported). Almost all variants occurred de novo, and most were truncating. Most affected individuals with protein-truncating variants presented with mild intellectual disability. One-quarter of individuals met criteria for autism. Additional common features include macrocephaly, hypotonia, functional gastrointestinal abnormalities, and a subtle facial gestalt. Epilepsy was present in about one-fifth of individuals with truncating variants and was responsive to treatment with anti-epileptic medications in almost all. More than 70% of the individuals were male, and expressivity was variable by sex; epilepsy was more common in females and autism more common in males. The four individuals with microdeletions encompassing KMT2E generally presented similarly to those with truncating variants, but the degree of developmental delay was greater. The group of four individuals with missense variants in KMT2E presented with the most severe developmental delays. Epilepsy was present in all individuals with missense variants, often manifesting as treatment-resistant infantile epileptic encephalopathy. Microcephaly was also common in this group. Haploinsufficiency versus gain-of-function or dominant-negative effects specific to these missense variants in KMT2E might explain this divergence in phenotype, but requires independent validation. Disruptive variants in KMT2E are an under-recognized cause of neurodevelopmental abnormalities.
Published: 2019
Full Text: View/download PDF

47. Defining and expanding the phenotype of

Author: Katrine M, Johannesen, Diana, Mitter, Robert, Janowski, Christian, Roth, Joseph, Toulouse, Anne-Lise, Poulat, Dorothee M, Ville, Nicolas, Chatron, Eva, Brilstra, Karin, Geleijns, Alfred Peter, Born, Scott, McLean, Kimberly, Nugent, Gareth, Baynam, Cathryn, Poulton, Lauren, Dreyer, Dylan, Gration, Solveig, Schulz, Andrea, Dieckmann, Katherine L, Helbig, Andreas, Merkenschlager, Rami, Jamra, Anja, Finck, Elena, Gardella, Helle, Hjalgrim, Ghayda, Mirzaa, Francesco, Brancati, Tatjana, Bierhals, Jonas, Denecke, Maja, Hempel, Johannes R, Lemke, Guido, Rubboli, Petra, Muschke, Renzo, Guerrini, Annalisa, Vetro, Dierk, Niessing, Gaetan, Lesca, and Rikke S, Møller
Subjects: Article
Abstract: Objective The study is aimed at widening the clinical and genetic spectrum and at assessing genotype-phenotype associations in QARS encephalopathy. Methods Through diagnostic gene panel screening in an epilepsy cohort, and recruiting through GeneMatcher and our international network, we collected 10 patients with biallelic QARS variants. In addition, we collected data on 12 patients described in the literature to further delineate the associated phenotype in a total cohort of 22 patients. Computer modeling was used to assess changes on protein folding. Results Biallelic pathogenic variants in QARS cause a triad of progressive microcephaly, moderate to severe developmental delay, and early-onset epilepsy. Microcephaly was present at birth in 65%, and in all patients at follow-up. Moderate (14%) or severe (73%) developmental delay was characteristic, with no achievement of sitting (85%), walking (86%), or talking (90%). Additional features included irritability (91%), hypertonia/spasticity (75%), hypotonia (83%), stereotypic movements (75%), and short stature (56%). Seventy-nine percent had pharmacoresistant epilepsy with mainly neonatal onset. Characteristic cranial MRI findings include early-onset progressive atrophy of cerebral cortex (89%) and cerebellum (61%), enlargement of ventricles (95%), and age-dependent delayed myelination (88%). A small subset of patients displayed a less severe phenotype. Conclusions These data revealed first genotype-phenotype associations and may serve for improved interpretation of new QARS variants and well-founded genetic counseling.
Published: 2019

48. Neuronal mechanisms of mutations in SCN8A causing epilepsy or intellectual disability

Author: Stephan Lauxmann, Yvonne G. Weber, Jan Benda, Yuanyuan Liu, Mahbubul Huq, Julian Schubert, Gerhard Kurlemann, Holger Lerche, Christina E. Hoei-Hansen, Felicitas Becker, Katherine L. Helbig, Elena Gardella, Lukas Sonnenberg, Michael C. Schneider, Mahmoud Koko, Katrine M Johannesen, Rikke S. Møller, and Maert Rannap
Subjects: 0301 basic medicine, SCN8A, Mutant, computational modelling, Mutation, Missense, Biology, medicine.disease_cause, Membrane Potentials, 03 medical and health sciences, Epilepsy, Mice, 0302 clinical medicine, Intellectual Disability, Intellectual disability, medicine, Animals, Humans, genetics, Cells, Cultured, Neurons, Mutation, Depolarization, medicine.disease, Phenotype, Rats, Mice, Inbred C57BL, Electrophysiology, 030104 developmental biology, nervous system, NAV1.6 Voltage-Gated Sodium Channel, intellectual disability, Autism, epilepsy, Neurology (clinical), Neuroscience, 030217 neurology & neurosurgery
Abstract: Ion channel mutations can cause distinct neuropsychiatric diseases. We first studied the biophysical and neurophysiological consequences of four mutations in the human Na+ channel gene SCN8A causing either mild (E1483K) or severe epilepsy (R1872W), or intellectual disability and autism without epilepsy (R1620L, A1622D). Only combined electrophysiological recordings of transfected wild-type or mutant channels in both neuroblastoma cells and primary cultured neurons revealed clear genotype-phenotype correlations. The E1483K mutation causing mild epilepsy showed no significant biophysical changes, whereas the R1872W mutation causing severe epilepsy induced clear gain-of-function biophysical changes in neuroblastoma cells. However, both mutations increased neuronal firing in primary neuronal cultures. In contrast, the R1620L mutation associated with intellectual disability and autism-but not epilepsy-reduced Na+ current density in neuroblastoma cells and expectedly decreased neuronal firing. Interestingly, for the fourth mutation, A1622D, causing severe intellectual disability and autism without epilepsy, we observed a dramatic slowing of fast inactivation in neuroblastoma cells, which induced a depolarization block in neurons with a reduction of neuronal firing. This latter finding was corroborated by computational modelling. In a second series of experiments, we recorded three more mutations (G1475R, M1760I, G964R, causing intermediate or severe epilepsy, or intellectual disability without epilepsy, respectively) that revealed similar results confirming clear genotype-phenotype relationships. We found intermediate or severe gain-of-function biophysical changes and increases in neuronal firing for the two epilepsy-causing mutations and decreased firing for the loss-of-function mutation causing intellectual disability. We conclude that studies in neurons are crucial to understand disease mechanisms, which here indicate that increased or decreased neuronal firing is responsible for distinct clinical phenotypes.
Published: 2019
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49. 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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50. Defining and expanding the phenotype of QARS-associated developmental epileptic encephalopathy

Author: Gareth Baynam, Christian Roth, Joseph Toulouse, Guido Rubboli, Karin Geleijns, Jonas Denecke, Robert Janowski, Dylan Gration, Diana Mitter, Alfred Peter Born, Dierk Niessing, Anne-Lise Poulat, Kimberly Nugent, Cathryn Poulton, Renzo Guerrini, Ghayda M. Mirzaa, Nicolas Chatron, Scott D. McLean, Eva H. Brilstra, H. Hjalgrim, Annalisa Vetro, Dorothée Ville, Rami Abou Jamra, Lauren Dreyer, Francesco Brancati, Katrine M Johannesen, Petra Muschke, Maja Hempel, Rikke S. Møller, Katherine L. Helbig, Gaetan Lesca, Anja Finck, Andrea Dieckmann, Tatjana Bierhals, E. Gardella, Andreas Merkenschlager, Solveig Schulz, and Johannes R. Lemke
Subjects: 0303 health sciences, Pediatrics, medicine.medical_specialty, Progressive microcephaly, Microcephaly, business.industry, Genetic counseling, Encephalopathy, medicine.disease, Irritability, Short stature, Hypotonia, 03 medical and health sciences, Epilepsy, 0302 clinical medicine, medicine, Neurology (clinical), medicine.symptom, business, 030217 neurology & neurosurgery, Genetics (clinical), 030304 developmental biology
Abstract: ObjectiveThe study is aimed at widening the clinical and genetic spectrum and at assessing genotype-phenotype associations in QARS encephalopathy.MethodsThrough diagnostic gene panel screening in an epilepsy cohort, and recruiting through GeneMatcher and our international network, we collected 10 patients with biallelic QARS variants. In addition, we collected data on 12 patients described in the literature to further delineate the associated phenotype in a total cohort of 22 patients. Computer modeling was used to assess changes on protein folding.ResultsBiallelic pathogenic variants in QARS cause a triad of progressive microcephaly, moderate to severe developmental delay, and early-onset epilepsy. Microcephaly was present at birth in 65%, and in all patients at follow-up. Moderate (14%) or severe (73%) developmental delay was characteristic, with no achievement of sitting (85%), walking (86%), or talking (90%). Additional features included irritability (91%), hypertonia/spasticity (75%), hypotonia (83%), stereotypic movements (75%), and short stature (56%). Seventy-nine percent had pharmacoresistant epilepsy with mainly neonatal onset. Characteristic cranial MRI findings include early-onset progressive atrophy of cerebral cortex (89%) and cerebellum (61%), enlargement of ventricles (95%), and age-dependent delayed myelination (88%). A small subset of patients displayed a less severe phenotype.ConclusionsThese data revealed first genotype-phenotype associations and may serve for improved interpretation of new QARS variants and well-founded genetic counseling.
Published: 2019
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