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1. LUSTR: a new customizable tool for calling genome-wide germline and somatic short tandem repeat variants

Author: Jinfeng Lu, Camilo Toro, David R. Adams, Undiagnosed Diseases Network, Cristiane Araujo Martins Moreno, Wan-Ping Lee, Yuk Yee Leung, Mathew B. Harms, Badri Vardarajan, and Erin L. Heinzen
Subjects: Short tandem repeats, Bioinformatics, Variant calling tool kit, Somatic, LUSTR, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract: Abstract Background Short tandem repeats (STRs) are widely distributed across the human genome and are associated with numerous neurological disorders. However, the extent that STRs contribute to disease is likely under-estimated because of the challenges calling these variants in short read next generation sequencing data. Several computational tools have been developed for STR variant calling, but none fully address all of the complexities associated with this variant class. Results Here we introduce LUSTR which is designed to address some of the challenges associated with STR variant calling by enabling more flexibility in defining STR loci, allowing for customizable modules to tailor analyses, and expanding the capability to call somatic and multiallelic STR variants. LUSTR is a user-friendly and easily customizable tool for targeted or unbiased genome-wide STR variant screening that can use either predefined or novel genome builds. Using both simulated and real data sets, we demonstrated that LUSTR accurately infers germline and somatic STR expansions in individuals with and without diseases. Conclusions LUSTR offers a powerful and user-friendly approach that allows for the identification of STR variants and can facilitate more comprehensive studies evaluating the role of pathogenic STR variants across human diseases.
Published: 2024
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2. Brain mosaicism of hedgehog signalling and other cilia genes in hypothalamic hamartoma

Author: Timothy E. Green, Atsushi Fujita, Navid Ghaderi, Erin L. Heinzen, Naomichi Matsumoto, Karl Martin Klein, Samuel F. Berkovic, and Michael S. Hildebrand
Subjects: Sonic hedgehog signalling, Hypothalamic hamartoma, Mosaicism, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571
Abstract: Hypothalamic hamartoma (HH) is a rare benign developmental brain lesion commonly associated with a well characterized epilepsy phenotype. Most individuals with HH are non-syndromic without additional developmental anomalies nor a family history of disease. Nonetheless, HH is a feature of Pallister-Hall (PHS) and Oro-Facial-Digital Type VI (OFD VI) syndromes, both characterized by additional developmental anomalies. Initial genetic of analysis HH began with syndromic HH, where germline inherited or de novo variants in GLI3, encoding a central transcription factor in the sonic hedgehog (Shh) signalling pathway, were identified in most individuals with PHS. Following these discoveries in syndromic HH, the hypothesis that post-zygotic mosaicism in related genes may underly non-syndromic HH was tested. We discuss the identified mosaic variants within individuals with non-syndromic HH, review the analytical methodologies and diagnostic yields, and explore understanding of the functional role of the implicated genes with respect to Shh signalling, and cilia development and function. We also outline future challenges in studying non-syndromic HH and suggest potential novel strategies to interrogate brain mosaicism in HH.
Published: 2023
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3. Mosaic variants detectable in blood extend the clinicogenetic spectrum of GLI3-related hypothalamic hamartoma

Author: Timothy E. Green, Mark F. Bennett, Ilka Immisch, Jeremy L. Freeman, Karl Martin Klein, John F. Kerrigan, Lata Vadlamudi, Erin L. Heinzen, Ingrid E. Scheffer, A. Simon Harvey, Felix Rosenow, Michael S. Hildebrand, and Samuel F. Berkovic
Subjects: GLI3 gene, Hypothalamic hamartoma, Mosaicism, Pallister-Hall syndrome, Polydactyly, Genetics, QH426-470, Medicine
Abstract: Purpose: Hypothalamic hamartoma (HH) can be syndromic (eg, Pallister-Hall syndrome [PHS], HH, and mesoaxial polydactyly) or nonsyndromic. Most PHS cases have germline variants in GLI3, but a minority remain unresolved. Some nonsyndromic HH cases have GLI3 mosaic variants in the brain. PHS and nonsyndromic HH are regarded as 2 separate GLI3-related disorders, clinically and genetically. Here, we searched for mosaic variants in unsolved cases. Methods: High-depth exome sequencing was performed on leukocyte-derived DNA in 1 unsolved PHS and 25 nonsyndromic HH cases. We searched for mosaic variants in GLI3 and other HH-associated genes. Mosaic variants were confirmed by droplet-digital polymerase chain reaction. Results: The PHS case had a GLI3 stop-gain variant c.2845G>T; p.(Glu949Ter) at 6.9% variant allele fraction (VAF). Two nonsyndromic cases had GLI3 variants—a stop-gain (c.2639C>A; p.(Ser880Ter), VAF 3.7%) and a frameshift (c.3326_3330del; p.(Glu1109AlafsTer18), VAF 7.8%). The nonsyndromic patient with 3.7% VAF in blood had 35.8% VAF in HH tissue. He had a vestigial extra digit removed adjacent to his left fifth finger. Conclusion: GLI3 mosaicism is associated with a phenotypic spectrum from PHS to HH with subtle extra PHS features, to isolated nonsyndromic HH. High-depth sequencing permits detection of low-level mosaicism, which is an important cause of both syndromic and nonsyndromic HH.
Published: 2023
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4. Common risk variants for epilepsy are enriched in families previously targeted for rare monogenic variant discovery

Author: Karen L. Oliver, Colin A. Ellis, Ingrid E. Scheffer, Shiva Ganesan, Costin Leu, Lynette G. Sadleir, Erin L. Heinzen, Heather C. Mefford, Andrew J. Bass, Sarah W. Curtis, Rebekah V. Harris, David C. Whiteman, Ingo Helbig, Ruth Ottman, Michael P. Epstein, Melanie Bahlo, and Samuel F. Berkovic
Subjects: Epilepsy genetics, Familial epilepsies, Common genetic variation, Polygenic risk scores, Medicine, Medicine (General), R5-920
Abstract: Summary: Background: The epilepsies are highly heritable conditions that commonly follow complex inheritance. While monogenic causes have been identified in rare familial epilepsies, most familial epilepsies remain unsolved. We aimed to determine (1) whether common genetic variation contributes to familial epilepsy risk, and (2) whether that genetic risk is enriched in familial compared with non-familial (sporadic) epilepsies. Methods: Using common variants derived from the largest epilepsy genome-wide association study, we calculated polygenic risk scores (PRS) for patients with familial epilepsy (n = 1,818 from 1,181 families), their unaffected relatives (n = 771), sporadic patients (n = 1,182), and population controls (n = 15,929). We also calculated separate PRS for genetic generalised epilepsy (GGE) and focal epilepsy. Statistical analyses used mixed-effects regression models to account for familial relatedness, sex, and ancestry. Findings: Patients with familial epilepsies had higher epilepsy PRS compared to population controls (OR 1·20, padj = 5×10−9), sporadic patients (OR 1·11, padj = 0.008), and their own unaffected relatives (OR 1·12, padj = 0.01). The top 1% of the PRS distribution was enriched 3.8-fold for individuals with familial epilepsy when compared to the lowest decile (padj = 5×10−11). Familial PRS enrichment was consistent across epilepsy type; overall, polygenic risk was greatest for the GGE clinical group. There was no significant PRS difference in familial cases with established rare variant genetic etiologies compared to unsolved familial cases. Interpretation: The aggregate effects of common genetic variants, measured as polygenic risk scores, play an important role in explaining why some families develop epilepsy, why specific family members are affected while their relatives are not, and why families manifest specific epilepsy types. Polygenic risk contributes to the complex inheritance of the epilepsies, including in individuals with a known genetic etiology. Funding: National Health and Medical Research Council of Australia, National Institutes of Health, American Academy of Neurology, Thomas B and Jeannette E Laws McCabe Fund, Mirowski Family Foundation.
Published: 2022
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5. A Novel Kv7.3 Variant in the Voltage-Sensing S4 Segment in a Family With Benign Neonatal Epilepsy: Functional Characterization and in vitro Rescue by β-Hydroxybutyrate

Author: Francesco Miceli, Lidia Carotenuto, Vincenzo Barrese, Maria Virginia Soldovieri, Erin L. Heinzen, Arthur M. Mandel, Natalie Lippa, Louise Bier, David B. Goldstein, Edward C. Cooper, Maria Roberta Cilio, Maurizio Taglialatela, and Tristan T. Sands
Subjects: KCNQ, BFNE, encephalopathy, channelopathies, ketogenic diet, Physiology, QP1-981
Abstract: Pathogenic variants in KCNQ2 and KCNQ3, paralogous genes encoding Kv7.2 and Kv7.3 voltage-gated K+ channel subunits, are responsible for early−onset developmental/epileptic disorders characterized by heterogeneous clinical phenotypes ranging from benign familial neonatal epilepsy (BFNE) to early−onset developmental and epileptic encephalopathy (DEE). KCNQ2 variants account for the majority of pedigrees with BFNE and KCNQ3 variants are responsible for a much smaller subgroup, but the reasons for this imbalance remain unclear. Analysis of additional pedigrees is needed to further clarify the nature of this genetic heterogeneity and to improve prediction of pathogenicity for novel variants. We identified a BFNE family with two siblings and a parent affected. Exome sequencing on samples from both parents and siblings revealed a novel KCNQ3 variant (c.719T>G; p.M240R), segregating in the three affected individuals. The M240 residue is conserved among human Kv7.2-5 and lies between the two arginines (R5 and R6) closest to the intracellular side of the voltage-sensing S4 transmembrane segment. Whole cell patch-clamp recordings in Chinese hamster ovary (CHO) cells revealed that homomeric Kv7.3 M240R channels were not functional, whereas heteromeric channels incorporating Kv7.3 M240R mutant subunits with Kv7.2 and Kv7.3 displayed a depolarizing shift of about 10 mV in activation gating. Molecular modeling results suggested that the M240R substitution preferentially stabilized the resting state and possibly destabilized the activated state of the Kv7.3 subunits, a result consistent with functional data. Exposure to β-hydroxybutyrate (BHB), a ketone body generated during the ketogenic diet (KD), reversed channel dysfunction induced by the M240R variant. In conclusion, we describe the first missense loss-of-function (LoF) pathogenic variant within the S4 segment of Kv7.3 identified in patients with BFNE. Studied under conditions mimicking heterozygosity, the M240R variant mainly affects the voltage sensitivity, in contrast to previously analyzed BFNE Kv7.3 variants that reduce current density. Our pharmacological results provide a rationale for the use of KD in patients carrying LoF variants in Kv7.2 or Kv7.3 subunits.
Published: 2020
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6. Annotating pathogenic non-coding variants in genic regions

Author: Sahar Gelfman, Quanli Wang, K. Melodi McSweeney, Zhong Ren, Francesca La Carpia, Matt Halvorsen, Kelly Schoch, Fanni Ratzon, Erin L. Heinzen, Michael J. Boland, Slavé Petrovski, and David B. Goldstein
Subjects: Science
Abstract: While non-coding synonymous and intronic variants are often not under strong selective constraint, they can be pathogenic through affecting splicing or transcription. Here, the authors develop a score that uses sequence context alterations to predict pathogenicity of synonymous and non-coding genetic variants, and provide a web server of pre-computed scores.
Published: 2017
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7. A functional correlate of severity in alternating hemiplegia of childhood

Author: Melody Li, Dana Jazayeri, Ben Corry, K. Melodi McSweeney, Erin L. Heinzen, David B. Goldstein, and Steven Petrou
Subjects: Na+/K+ ATPase, Alternating hemiplegia of childhood, ATP1A3, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571
Abstract: Objective: Mutations in ATP1A3, the gene that encodes the α3 subunit of the Na+/K+ ATPase, are the primary cause of alternating hemiplegia of childhood (AHC). Correlations between different mutations and AHC severity were recently reported, with E815K identified in severe and D801N and G947R in milder cases. This study aims to explore the molecular pathological mechanisms in AHC and to identify functional correlates for mutations associated with different levels of disease severity. Methods: Human wild type ATP1A3, and E815K, D801N and G947R mutants were expressed in Xenopus laevis oocytes and Na+/K+ ATPase function measured. Structural homology models of the human α3 subunit containing AHC mutations were created. Results: The AHC mutations examined all showed similar levels of reduction in forward cycling. Wild type forward cycling was reduced by coexpression with any mutant, indicating dominant negative interactions. Proton transport was measured and found to be selectively impaired only in E815K. Homology modeling showed that D801 and G947 lie within or near known cation binding sites while E815 is more distal. Despite its effect on proton transport, E815K was also distant from the proposed proton transport route. Interpretation: Loss of forward cycling and dominant negativity are common and likely necessary pathomechanisms for AHC. In addition, loss of proton transport correlated with severity of AHC. D801N and G947R are likely to directly disrupt normal Na+/K+ binding while E815K may disrupt forward cycling and proton transport via allosteric mechanisms yet to be elucidated.
Published: 2015
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8. Correction: Genic Intolerance to Functional Variation and the Interpretation of Personal Genomes.

Author: Slavé Petrovski, Quanli Wang, Erin L. Heinzen, Andrew S. Allen, and David B. Goldstein
Subjects: Genetics, QH426-470
Published: 2013
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9. Correction: A Genome-Wide Investigation of SNPs and CNVs in Schizophrenia.

Author: Anna C. Need, Dongliang Ge, Michael E. Weale, Jessica Maia, Sheng Feng, Erin L. Heinzen, Kevin V. Shianna, Woohyun Yoon, Dalia Kasperavičiūtė, Massimo Gennarelli, Warren J. Strittmatter, Cristian Bonvicini, Giuseppe Rossi, Karu Jayathilake, Philip A. Cola, Joseph P. McEvoy, Richard S. E. Keefe, Elizabeth M. C. Fisher, Pamela L. St. Jean, Ina Giegling, Annette M. Hartmann, Hans-Jürgen Möller, Andreas Ruppert, Gillian Fraser, Caroline Crombie, Lefkos T. Middleton, David St. Clair, Allen D. Roses, Pierandrea Muglia, Clyde Francks, Dan Rujescu, Herbert Y. Meltzer, and David B. Goldstein
Subjects: Genetics, QH426-470
Published: 2009
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10. Somatic variants in diverse genes leads to a spectrum of focal cortical malformations

Author: Dulcie Lai, Meethila Gade, Edward Yang, Hyun Yong Koh, Jinfeng Lu, Nicole M Walley, Anne F Buckley, Tristan T Sands, Cigdem I Akman, Mohamad A Mikati, Guy M McKhann, James E Goldman, Peter Canoll, Allyson L Alexander, Kristen L Park, Gretchen K Von Allmen, Olga Rodziyevska, Meenakshi B Bhattacharjee, Hart G W Lidov, Hannes Vogel, Gerald A Grant, Brenda E Porter, Annapurna H Poduri, Peter B Crino, and Erin L Heinzen
Subjects: Epilepsy, TOR Serine-Threonine Kinases, Cell Cycle Proteins, Cadherins, Protocadherins, Hemimegalencephaly, Malformations of Cortical Development, Phosphatidylinositol 3-Kinases, Malformations of Cortical Development, Group I, Mutation, Humans, Female, Original Article, Neurology (clinical), Proto-Oncogene Proteins c-akt
Abstract: Post-zygotically acquired genetic variants, or somatic variants, that arise during cortical development have emerged as important causes of focal epilepsies, particularly those due to malformations of cortical development. Pathogenic somatic variants have been identified in many genes within the PI3K-AKT-mTOR-signalling pathway in individuals with hemimegalencephaly and focal cortical dysplasia (type II), and more recently in SLC35A2 in individuals with focal cortical dysplasia (type I) or non-dysplastic epileptic cortex. Given the expanding role of somatic variants across different brain malformations, we sought to delineate the landscape of somatic variants in a large cohort of patients who underwent epilepsy surgery with hemimegalencephaly or focal cortical dysplasia. We evaluated samples from 123 children with hemimegalencephaly (n = 16), focal cortical dysplasia type I and related phenotypes (n = 48), focal cortical dysplasia type II (n = 44), or focal cortical dysplasia type III (n = 15). We performed high-depth exome sequencing in brain tissue-derived DNA from each case and identified somatic single nucleotide, indel and large copy number variants. In 75% of individuals with hemimegalencephaly and 29% with focal cortical dysplasia type II, we identified pathogenic variants in PI3K-AKT-mTOR pathway genes. Four of 48 cases with focal cortical dysplasia type I (8%) had a likely pathogenic variant in SLC35A2. While no other gene had multiple disease-causing somatic variants across the focal cortical dysplasia type I cohort, four individuals in this group had a single pathogenic or likely pathogenic somatic variant in CASK, KRAS, NF1 and NIPBL, genes previously associated with neurodevelopmental disorders. No rare pathogenic or likely pathogenic somatic variants in any neurological disease genes like those identified in the focal cortical dysplasia type I cohort were found in 63 neurologically normal controls (P = 0.017), suggesting a role for these novel variants. We also identified a somatic loss-of-function variant in the known epilepsy gene, PCDH19, present in a small number of alleles in the dysplastic tissue from a female patient with focal cortical dysplasia IIIa with hippocampal sclerosis. In contrast to focal cortical dysplasia type II, neither focal cortical dysplasia type I nor III had somatic variants in genes that converge on a unifying biological pathway, suggesting greater genetic heterogeneity compared to type II. Importantly, we demonstrate that focal cortical dysplasia types I, II and III are associated with somatic gene variants across a broad range of genes, many associated with epilepsy in clinical syndromes caused by germline variants, as well as including some not previously associated with radiographically evident cortical brain malformations.
Published: 2022

11. Sporadic hypothalamic hamartoma is a ciliopathy with somatic and bi-allelic contributions

Author: Timothy E Green, Joshua E Motelow, Mark F Bennett, Zimeng Ye, Caitlin A Bennett, Nicole G Griffin, John A Damiano, Richard J Leventer, Jeremy L Freeman, A Simon Harvey, Paul J Lockhart, Lynette G Sadleir, Amber Boys, Ingrid E Scheffer, Heather Major, Benjamin W Darbro, Melanie Bahlo, David B Goldstein, John F Kerrigan, Erin L Heinzen, Samuel F Berkovic, and Michael S Hildebrand
Subjects: congenital, hereditary, and neonatal diseases and abnormalities, Hamartoma, Genetics, Humans, Original Article, Hedgehog Proteins, General Medicine, Magnetic Resonance Imaging, Molecular Biology, Ciliopathies, Hypothalamic Diseases, Genetics (clinical)
Abstract: Hypothalamic hamartoma with gelastic seizures is a well-established cause of drug-resistant epilepsy in early life. The development of novel surgical techniques has permitted the genomic interrogation of hypothalamic hamartoma tissue. This has revealed causative mosaic variants within GLI3, OFD1 and other key regulators of the sonic-hedgehog pathway in a minority of cases. Sonic-hedgehog signalling proteins localize to the cellular organelle primary cilia. We therefore explored the hypothesis that cilia gene variants may underlie hitherto unsolved cases of sporadic hypothalamic hamartoma. We performed high-depth exome sequencing and chromosomal microarray on surgically resected hypothalamic hamartoma tissue and paired leukocyte-derived DNA from 27 patients. We searched for both germline and somatic variants under both dominant and bi-allelic genetic models. In hamartoma-derived DNA of seven patients we identified bi-allelic (one germline, one somatic) variants within one of four cilia genes—DYNC2I1, DYNC2H1, IFT140 or SMO. In eight patients, we identified single somatic variants in the previously established hypothalamic hamartoma disease genes GLI3 or OFD1. Overall, we established a plausible molecular cause for 15/27 (56%) patients. Here, we expand the genetic architecture beyond single variants within dominant disease genes that cause sporadic hypothalamic hamartoma to bi-allelic (one germline/one somatic) variants, implicate three novel cilia genes and reconceptualize the disorder as a ciliopathy.
Published: 2022

12. The benefit of diagnostic whole genome sequencing in schizophrenia and other psychotic disorders

Author: Anna R. Docherty, Vimla Aggarwal, James M. McNamara, Ayan Malakar, Daniel Hughes, Andrey A. Shabalin, Anat Grossman-Jonish, Lior Greenbaum, Gundula Povysil, Shannon Delaney, Hann-Shyan Hwang, Evan H. Baugh, David Goldstein, Anna Alkelai, Emma P. Peabody, Matthew B. Harms, Sahar Gelfman, Bernard Lerer, Vaidehi Jobanputra, Ann E. Pulver, Anthony W. Zoghbi, and Erin L. Heinzen
Subjects: Proband, education.field_of_study, medicine.medical_specialty, Candidate gene, Psychosis, business.industry, Genetic counseling, Population, Schizoaffective disorder, medicine.disease, Cellular and Molecular Neuroscience, Psychiatry and Mental health, Schizophrenia, Internal medicine, medicine, Copy-number variation, education, business, Molecular Biology
Abstract: Schizophrenia has a multifactorial etiology, involving a polygenic architecture. The potential benefit of whole genome sequencing (WGS) in schizophrenia and other psychotic disorders is not well studied. We investigated the yield of clinical WGS analysis in 251 families with a proband diagnosed with schizophrenia (N = 190), schizoaffective disorder (N = 49), or other conditions involving psychosis (N = 48). Participants were recruited in Israel and USA, mainly of Jewish, Arab, and other European ancestries. Trio (parents and proband) WGS was performed for 228 families (90.8%); in the other families, WGS included parents and at least two affected siblings. In the secondary analyses, we evaluated the contribution of rare variant enrichment in particular gene sets, and calculated polygenic risk score (PRS) for schizophrenia. For the primary outcome, diagnostic rate was 6.4%; we found clinically significant, single nucleotide variants (SNVs) or small insertions or deletions (indels) in 14 probands (5.6%), and copy number variants (CNVs) in 2 (0.8%). Significant enrichment of rare loss-of-function variants was observed in a gene set of top schizophrenia candidate genes in affected individuals, compared with population controls (N = 6,840). The PRS for schizophrenia was significantly increased in the affected individuals group, compared to their unaffected relatives. Last, we were also able to provide pharmacogenomics information based on CYP2D6 genotype data for most participants, and determine their antipsychotic metabolizer status. In conclusion, our findings suggest that WGS may have a role in the setting of both research and genetic counseling for individuals with schizophrenia and other psychotic disorders and their families.
Published: 2021

13. Somatic Ras/Raf/MAPK Variants Enriched in the Hippocampus in Drug-Resistant Mesial Temporal Lobe Epilepsy

Author: Sattar Khoshkhoo, Yilan Wang, Yasmine Chahine, E. Zeynep Erson-Omay, Stephanie Robert, Emre Kiziltug, Eyiyemisi C. Damisah, Carol Nelson-Williams, Guangya Zhu, Wenna Kong, August Yue Huang, Edward Stronge, H. Westley Phillips, Brian H. Chhouk, Sara Bizzotto, Ming Hui Chen, Thiuni N. Adikari, Zimeng Ye, Tom Witkowski, Dulcie Lai, Nadine Lee, Julie Lokan, Ingrid E. Scheffer, Samuel F. Berkovic, Shozeb Haider, Michael S. Hildebrand, Edward Yang, Murat Gunel, Richard P. Lifton, R Mark Richardson, Ingmar Blümcke, Sanda Alexandrescu, Anita Huttner, Erin L. Heinzen, Jidong Zhu, Annapurna Poduri, Nihal DeLanerolle, Dennis D. Spencer, Eunjung Alice Lee, Christopher A. Walsh, and Kristopher T. Kahle
Abstract: ImportanceMesial temporal lobe epilepsy (MTLE) is the most common focal epilepsy subtype and is often refractory to anti-seizure medications. While most MTLE patients do not have pathogenic germline genetic variants, the contribution of post-zygotic (i.e., somatic) variants in the brain is unknown.ObjectiveTo test the association between pathogenic somatic variants in the hippocampus and MTLE.DesignThis case-control genetic association study analyzed the DNA derived from hippocampal tissue of neurosurgically-treated patients with MTLE and age- and sex-matched neurotypical controls. Participants were enrolled from 1988 through 2019 and clinical data was collected retrospectively. Whole-exome and gene-panel sequencing (depth>500X) were used to identify candidate pathogenic somatic variants. A subset of novel variants were functionally evaluated using cellular and molecular assays.SettingLevel 4 epilepsy centers, multi-center study.ParticipantsNon-lesional and lesional (mesial temporal sclerosis, focal cortical dysplasia, and low-grade epilepsy-associated tumors) drug-resistant MTLE patients who underwent anterior medial temporal lobectomy. All patients with available frozen tissue and appropriate consents were included. Control brain tissue was obtained from neurotypical donors at brain banks.ExposuresDrug-resistant MTLE.Main Outcomes and MeasuresPresence and abundance of pathogenic somatic variants in the hippocampus versus the unaffected temporal neocortex.ResultsSamples were obtained from 105 MTLE patients (52 male, 53 female; age: MED [IQR], 32 [26-44]) and 30 neurotypical controls (19 male, 11 female; age: MED [IQR], 37 [18-53]). Eleven pathogenic somatic variants, enriched in the hippocampus relative to the unaffected temporal neocortex (MED [IQR], 1.92 [1.5-2.7] vs 0.3 [0-0.9], pPTPN11, SOS1, KRAS, BRAF, andNF1, all predicted to constitutively activate Ras/Raf/MAPK signaling. Immunohistochemical studies of variant-positive hippocampal tissue demonstrated increased Erk1/2 phosphorylation, indicative of Ras/Raf/MAPK activation, predominantly in glial cells. Molecular assays showed abnormal liquid-liquid phase separation for thePTPN11variants as a possible dominant gain-of-function mechanism.Conclusions and RelevanceHippocampal somatic variants, particularly those activating Ras/Raf/MAPK signaling, may contribute to the pathogenesis of sporadic, drug-resistant MTLE. These findings may provide a novel genetic mechanism and highlight new therapeutic targets for this common indication for epilepsy surgery.
Published: 2022

14. Rare Genetic Variation and Outcome of Surgery for Mesial Temporal Lobe Epilepsy

Author: Piero, Perucca, Kate, Stanley, Natasha, Harris, Anne M, McIntosh, Ali A, Asadi-Pooya, Mohamad A, Mikati, Danielle M, Andrade, Patricia, Dugan, Chantal, Depondt, Hyunmi, Choi, Erin L, Heinzen, Gianpiero L, Cavalleri, Russell J, Buono, Orrin, Devinsky, Michael R, Sperling, Samuel F, Berkovic, Norman, Delanty, David B, Goldstein, and Terence J, O'Brien
Subjects: Neurology, Neurology (clinical)
Abstract: Genetic factors have long been debated as a cause of failure of surgery for mesial temporal lobe epilepsy (MTLE). We investigated whether rare genetic variation influences seizure outcomes of MTLE surgery.We performed an international, multicenter, whole exome sequencing study of patients who underwent surgery for drug-resistant, unilateral MTLE with normal magnetic resonance imaging (MRI) or MRI evidence of hippocampal sclerosis and ≥2-year postsurgical follow-up. Patients with either sustained seizure freedom (favorable outcome) or ongoing uncontrolled seizures since surgery (unfavorable outcome) were included. Exomes of controls without epilepsy were also included. Gene set burden analyses were carried out to identify genes with significant enrichment of rare deleterious variants in patients compared to controls.Nine centers from 3 continents contributed 206 patients operated for drug-resistant unilateral MTLE, of whom 196 (149 with favorable outcome and 47 with unfavorable outcome) were included after stringent quality control. Compared to 8,718 controls, MTLE cases carried a higher burden of ultrarare missense variants in constrained genes that are intolerant to loss-of-function (LoF) variants (odds ratio [OR] = 2.6, 95% confidence interval [CI] = 1.9-3.5, p = 1.3E-09) and in genes encoding voltage-gated cation channels (OR = 2.4, 95% CI = 1.4-3.8, p = 2.7E-04). Proportions of subjects with such variants were comparable between patients with favorable outcome and those with unfavorable outcome, with no significant between-group differences.Rare variation contributes to the genetic architecture of MTLE, but does not appear to have a major role in failure of MTLE surgery. These findings can be incorporated into presurgical decision-making and counseling. ANN NEUROL 2022.
Published: 2022

15. CSNK2B

Author: Judith Bluvstein, Suneeta Madan-Khetarpal, Daniel Groepper, Theodore Sheehan, Michael J. Lyons, Louise Bier, Julie Fleischer, Annapurna Poduri, Lynn Pais, Pascal Joset, Elena Infante, Evan H. Baugh, David Goldstein, Tristan T. Sands, Katharina Steindl, Pim Suwannarat, Cyril Mignot, Boris Keren, Matthew J. Ferber, Laura Schultz-Rogers, Natalie Lippa, Linda Hasadsri, Vinodh Narayanan, Maureen S. Mulhern, Alejandra Vasquez, Claudia A. L. Ruivenkamp, Marleen Simon, Susan M. White, Vimla Aggarwal, Eric W. Klee, Kristine K. Bachman, Lindsay C. Burrage, Caroline Nava, Nicholas Stong, Neil A. Hanchard, Josephine S.C. Chong, Anita Rauch, Renee Bend, Erin L. Heinzen, Sulagna Kushary, Marije Koopmans, Marissa S. Ellingson, Keri Ramsey, Raymond Yeh, Michelle E. Ernst, Ellen van Binsbergen, Sarah S. Barnett, Amanda Thomas, Kristin G. Monaghan, Eva H. Brilstra, Magalie S. Leduc, Weimin Bi, Jennifer A. Lee, Cigdem I. Akman, Sophie Mathieu, Andrea H. Seeley, Grazia M. S. Mancini, and Clinical Genetics
Subjects: 0301 basic medicine, Adult, Male, Pediatrics, medicine.medical_specialty, Adolescent, CK2, Developmental Disabilities, Epilepsies, Myoclonic, Status epilepticus, casein kinase II, Article, MSNE, 03 medical and health sciences, Broad spectrum, Epilepsy, Young Adult, 0302 clinical medicine, Status Epilepticus, Intellectual Disability, Intellectual disability, medicine, Humans, Exome, Generalized epilepsy, Age of Onset, generalized epilepsy, Child, Exome sequencing, business.industry, Genetic Variation, Infant, medicine.disease, Young age, 030104 developmental biology, myoclonic status epilepticus, Phenotype, Neurology, Child, Preschool, Mutation, myoclonic seizures, Epilepsy, Generalized, Female, Neurology (clinical), medicine.symptom, Epilepsy severity, business, 030217 neurology & neurosurgery
Abstract: CSNK2B has recently been implicated as a disease gene for neurodevelopmental disability (NDD) and epilepsy. Information about developmental outcomes has been limited by the young age and short follow-up for many of the previously reported cases, and further delineation of the spectrum of associated phenotypes is needed. We present 25 new patients with variants in CSNK2B and refine the associated NDD and epilepsy phenotypes. CSNK2B variants were identified by research or clinical exome sequencing, and investigators from different centers were connected via GeneMatcher. Most individuals had developmental delay and generalized epilepsy with onset in the first 2 years. However, we found a broad spectrum of phenotypic severity, ranging from early normal development with pharmacoresponsive seizures to profound intellectual disability with intractable epilepsy and recurrent refractory status epilepticus. These findings suggest that CSNK2B should be considered in the diagnostic evaluation of patients with a broad range of NDD with treatable or intractable seizures.
Published: 2021

16. De novo TRIM8 variants impair its protein localization to nuclear bodies and cause developmental delay, epilepsy, and focal segmental glomerulosclerosis

Author: Verena Klämbt, Youying Mao, Vimla Aggarwal, Arang Kim, Friedhelm Hildebrandt, Mohamad A. Mikati, Vandana Shashi, Anne H. O’Donnell-Luria, Vaidehi Jobanputra, Jeremiah Martino, Vivette D. D'Agati, Minxian Wang, Marcus R. Benz, Shoji Yano, Janine Altmüller, Ali G. Gharavi, Florian Buerger, Enrico Fiaccadori, Richard P. Lifton, Bodo B. Beck, Amy Kolb, Mordi Muorah, David Goldstein, Nina Mann, Martin R. Pollak, Dina Ahram, Heidi Cope, Gian Marco Ghiggeri, Jillian S. Parboosingh, Asmaa S. AbuMaziad, Kamal Khan, Ana C. Onuchic-Whitford, Louise Bier, Emma Pierce-Hoffman, Jonathan E. Zuckerman, Shrikant Mane, Moin A. Saleem, Amar J. Majmundar, Heidi L. Rehm, Ora Yadin, Erin L. Heinzen, Gina Y. Jin, Christelle Moufawad El Achkar, Konstantin Deutsch, Julia Hoefele, Ania Koziell, Gianluca Caridi, Talha Gunduz, Agnieszka Bierzynska, Korbinian M. Riedhammer, Monica Bodria, Ronen Schneider, Julian A. Martinez-Agosto, Thomas M. Kitzler, Shirlee Shril, Ulrike John-Kroegel, Howard Trachtman, Adele Mitrotti, Eleanor G. Seaby, Amanda V. Tyndall, Isabella Pisani, Patricia L. Weng, Tze Y Lim, A. Micheil Innes, John Musgrove, Simone Sanna-Cherchi, and Erica E. Davis
Subjects: Adult, Male, 0301 basic medicine, Proband, medicine.medical_specialty, Nephrotic Syndrome, Developmental Disabilities, 030232 urology & nephrology, Neurogenetics, Nerve Tissue Proteins, Biology, Kidney, Cell Line, Mice, 03 medical and health sciences, Exon, 0302 clinical medicine, Focal segmental glomerulosclerosis, Report, Exome Sequencing, Genetics, medicine, Animals, Humans, Child, Exome, Genetics (clinical), Exome sequencing, Epilepsy, Glomerulosclerosis, Focal Segmental, Podocytes, medicine.disease, 3. Good health, Phenotype, 030104 developmental biology, Codon, Nonsense, Child, Preschool, Mutation, Medical genetics, Female, Intranuclear Space, Carrier Proteins, Nephrotic syndrome
Abstract: Focal segmental glomerulosclerosis (FSGS) is the main pathology underlying steroid-resistant nephrotic syndrome (SRNS) and a leading cause of chronic kidney disease. Monogenic forms of pediatric SRNS are predominantly caused by recessive mutations, while the contribution of de novo variants (DNVs) to this trait is poorly understood. Using exome sequencing (ES) in a proband with FSGS/SRNS, developmental delay, and epilepsy, we discovered a nonsense DNV in TRIM8, which encodes the E3 ubiquitin ligase tripartite motif containing 8. To establish whether TRIM8 variants represent a cause of FSGS, we aggregated exome/genome-sequencing data for 2,501 pediatric FSGS/SRNS-affected individuals and 48,556 control subjects, detecting eight heterozygous TRIM8 truncating variants in affected subjects but none in control subjects (p = 3.28 × 10(−11)). In all six cases with available parental DNA, we demonstrated de novo inheritance (p = 2.21 × 10(−15)). Reverse phenotyping revealed neurodevelopmental disease in all eight families. We next analyzed ES from 9,067 individuals with epilepsy, yielding three additional families with truncating TRIM8 variants. Clinical review revealed FSGS in all. All TRIM8 variants cause protein truncation clustering within the last exon between residues 390 and 487 of the 551 amino acid protein, indicating a correlation between this syndrome and loss of the TRIM8 C-terminal region. Wild-type TRIM8 overexpressed in immortalized human podocytes and neuronal cells localized to nuclear bodies, while constructs harboring patient-specific variants mislocalized diffusely to the nucleoplasm. Co-localization studies demonstrated that Gemini and Cajal bodies frequently abut a TRIM8 nuclear body. Truncating TRIM8 DNVs cause a neuro-renal syndrome via aberrant TRIM8 localization, implicating nuclear bodies in FSGS and developmental brain disease.
Published: 2021

17. Mosaic variants detectable in blood extend the clinico-genetic spectrum of GLI3-related Hypothalamic Hamartoma

Author: Timothy E. Green, Mark F. Bennett, Ilka Immisch, Jeremy L. Freeman, Karl Martin Klein, John F. Kerrigan, Lata Vadlamudi, Erin L. Heinzen, Ingrid E. Scheffer, A. Simon Harvey, Felix Rosenow, Michael S. Hildebrand, and Samuel F. Berkovic
Published: 2023

18. Epilepsy Genetics: Advancements in the Field and Impact on Clinical Practice

Author: Senyene E. Hunter, Elizabeth Jalazo, Thomas R. Felton, Erin L. Heinzen, and Yael Shiloh-Malawsky
Published: 2022

19. A pharmacogenomic assessment of psychiatric adverse drug reactions to levetiracetam

Author: Ciarán, Campbell, Mark, McCormack, Sonn, Patel, Caragh, Stapleton, Dheeraj, Bobbili, Roland, Krause, Chantal, Depondt, Graeme J, Sills, Bobby P, Koeleman, Pasquale, Striano, Federico, Zara, Josemir W, Sander, Holger, Lerche, Wolfram S, Kunz, Kari, Stefansson, Hreinn, Stefansson, Colin P, Doherty, Erin L, Heinzen, Ingrid E, Scheffer, David B, Goldstein, Terence, O'Brien, David, Cotter, Samuel F, Berkovic, Sanjay M, Sisodiya, Norman, Delanty, and Gianpiero L, Cavalleri
Subjects: pharmacogenomics, adverse drug reactions, Anticonvulsants/adverse effects, Neurologie [D14] [Sciences de la santé humaine], Levetiracetam, Drug-Related Side Effects and Adverse Reactions, Genetic Predisposition to Disease/genetics, levetiracetam, Neurology [D14] [Human health sciences], Neurology, Pharmacogenetics, Levetiracetam/adverse effects, Case-Control Studies, Humans, Anticonvulsants, Genetic Predisposition to Disease, Neurology (clinical), psychosis, Prospective Studies, polygenic risk scoring, Genome-Wide Association Study
Abstract: OBJECTIVE: Levetiracetam (LEV) is an effective antiseizure medicine, but 10%-20% of people treated with LEV report psychiatric side-effects, and up to 1% may have psychotic episodes. Pharmacogenomic predictors of these adverse drug reactions (ADRs) have yet to be identified. We sought to determine the contribution of both common and rare genetic variation to psychiatric and behavioral ADRs associated with LEV. METHODS: This case-control study compared cases of LEV-associated behavioral disorder (n = 149) or psychotic reaction (n = 37) to LEV-exposed people with no history of psychiatric ADRs (n = 920). All samples were of European ancestry. We performed genome-wide association study (GWAS) analysis comparing those with LEV ADRs to controls. We estimated the polygenic risk scores (PRS) for schizophrenia and compared cases with LEV-associated psychotic reaction to controls. Rare variant burden analysis was performed using exome sequence data of cases with psychotic reactions (n = 18) and controls (n = 122). RESULTS: Univariate GWAS found no significant associations with either LEV-associated behavioural disorder or LEV-psychotic reaction. PRS analysis showed that cases of LEV-associated psychotic reaction had an increased PRS for schizophrenia relative to contr ols (p = .0097, estimate = .4886). The rare-variant analysis found no evidence of an increased burden of rare genetic variants in people who had experienced LEV-associated psychotic reaction relative to controls. SIGNIFICANCE: The polygenic burden for schizophrenia is a risk factor for LEV-associated psychotic reaction. To assess the clinical utility of PRS as a predictor, it should be tested in an independent and ideally prospective cohort. Larger sample sizes are required for the identification of significant univariate common genetic signals or rare genetic signals associated with psychiatric LEV ADRs.
Published: 2022

20. Expansion of the GRIA2 phenotypic representation: a novel de novo loss of function mutation in a case with childhood onset schizophrenia

Author: Yoav Kohn, Neha Dagaonkar, Shlomit Rienstein, David Goldstein, Shahar Shohat, Eti Chitrit-Raveh, Erin L. Heinzen, Vimla S. Aggarwal, Sagiv Shifman, Anna Alkelai, Tanya Schechter, Daniel Hughes, Benjamin Draiman, and Lior Greenbaum
Subjects: 0301 basic medicine, Genetics, AMPA receptor, 030105 genetics & heredity, Biology, medicine.disease, Phenotype, 03 medical and health sciences, Epilepsy, 030104 developmental biology, Schizophrenia, Autism spectrum disorder, Intellectual disability, medicine, biology.protein, GRIA2, Genetics (clinical), Loss function
Abstract: Childhood-onset schizophrenia (COS) is a rare form of schizophrenia with an onset before 13 years of age. There is rising evidence that genetic factors play a major role in COS etiology, yet, only a few single gene mutations have been discovered. Here we present a diagnostic whole-exome sequencing (WES) in an Israeli Jewish female with COS and additional neuropsychiatric conditions such as obsessive-compulsive disorder (OCD), anxiety, and aggressive behavior. Variant analysis revealed a de novo novel stop gained variant in GRIA2 gene (NM_000826.4: c.1522 G > T (p.Glu508Ter)). GRIA2 encodes for a subunit of the AMPA sensitive glutamate receptor (GluA2) that functions as ligand-gated ion channel in the central nervous system and plays an important role in excitatory synaptic transmission. GluA2 subunit mutations are known to cause variable neurodevelopmental phenotypes including intellectual disability, autism spectrum disorder, epilepsy, and OCD. Our findings support the potential diagnostic role of WES in COS, identify GRIA2 as possible cause to a broad psychiatric phenotype that includes COS as a major manifestation and expand the previously reported GRIA2 loss of function phenotypes.
Published: 2020

21. Somatic mutation involving diverse genes leads to a spectrum of focal cortical malformations

Author: Dulcie Lai, Meethila Gade, Edward Yang, Hyun Yong Koh, Nicole M. Walley, Anne F. Buckley, Tristan T. Sands, Cigdem I. Akman, Mohamad A. Mikati, Guy M. McKhann, James E. Goldman, Peter D. Canoll, Allyson L. Alexander, Kristen L. Park, Gretchen K. Von Allmen, Meenakshi B. Bhattacharjee, Hart G.W. Lidov, Hannes Vogel, Gerald A. Grant, Brenda E. Porter, Annapurna H. Poduri, Peter B. Crino, and Erin L. Heinzen
Abstract: Post-zygotically acquired genetic variants, or somatic variants, that arise during cortical development have emerged as important causes of focal epilepsies, particularly those due to malformations of cortical development. Pathogenic somatic variants have been identified in many genes within the PI3K-AKT3-mTOR-signaling pathway in individuals with hemimegalencephaly and focal cortical dysplasia (type II), and more recently in SLC35A2 in individuals with focal cortical dysplasia (type I) or non-dysplastic epileptic cortex. Given the expanding role of somatic variants across different brain malformations, we sought to delineate the landscape of somatic variants in a large cohort of patients who underwent epilepsy surgery with hemimegalencephaly or focal cortical dysplasia. We evaluated samples from 123 children with hemimegalencephaly (n=16), focal cortical dysplasia type I and related phenotypes (n=48), focal cortical dysplasia type II (n=44), or focal cortical dysplasia type III (n=15) classified using imaging and pathological findings. We performed high-depth exome sequencing in brain tissue-derived DNA from each case and identified somatic single nucleotide, indel, and large copy number variants. In 75% of individuals with hemimegalencephaly and 29% with focal cortical dysplasia type II, we identified pathogenic variants in PI3K-AKT-mTOR pathway genes. Four of 48 cases with focal cortical dysplasia type I (8%) had a likely pathogenic variant in SLC35A2. While no other gene had multiple disease-causing somatic variants across the focal cortical dysplasia type I cohort, four individuals in this group had a single pathogenic or likely pathogenic somatic variant in CASK, KRAS, NF1, and NIPBL, genes associated with neurodevelopmental disorders. No rare pathogenic or likely pathogenic somatic variants in any neurological disease genes like those identified in the focal cortical dysplasia type I cohort were found in 63 neurologically normal controls (P = 0.017), suggesting a role for these novel variants. We also identified a somatic loss-of-function variant in the known epilepsy gene, PCDH19, present in a very small number of alleles in the dysplastic tissue from a female patient with focal cortical dysplasia IIIa with hippocampal sclerosis. In contrast to focal cortical dysplasia type II, neither focal cortical dysplasia type I nor III had somatic variants in genes that converge on a unifying biological pathway, suggesting greater genetic heterogeneity compared to type II. Importantly, we demonstrate that FCD types I, II, and III, are associated with somatic gene variants across a broad range of genes, many associated with epilepsy in clinical syndromes caused by germline variants, as well as including some not previously associated with radiographically evident cortical brain malformations.
Published: 2021

22. How We Got to Where We're Going

Author: Annapurna H. Poduri, Alfred L. George Jr, Erin L. Heinzen, Daniel Lowenstein, and Sara James
Abstract: This Element serves as a welcome to the Cambridge Elements Genetics in Epilepsy series. The series editors look forward to sharing with you the story of epilepsy genetics through a series of Elements. They will bring together many voices, by text as well as video, to illustrate the history of epilepsy genetics, the many on-going efforts in the field, and how they hope to address the still unanswered questions that command the attention of all of us and our colleagues across the globe.
Published: 2021

23. SVA: software for annotating and visualizing sequenced human genomes.

Author: Dongliang Ge, Elizabeth K. Ruzzo, Kevin V. Shianna, Min He, Kimberly Pelak, Erin L. Heinzen, Anna C. Need, Elizabeth T. Cirulli, Jessica M. Maia, Samuel P. Dickson, Mingfu Zhu, Abanish Singh, Andrew S. Allen, and David B. Goldstein
Published: 2011
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24. 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

25. Quantitative analysis of phenotypic elements augments traditional electroclinical classification of common familial epilepsies

Author: Orrin Devinsky, Samuel F. Berkovic, Catharine Freyer, Annapurna Poduri, Eric B. Geller, Amos D. Korczyn, Heidi E. Kirsch, Nathan B. Fountain, Rosemary Burgess, Jack M. Parent, Jocelyn F. Bautista, Susannah T. Bellows, Robert C. Knowlton, David Goldstein, Dennis J. Dlugos, Heather C Mefford, Anthony G Marson, Mike Smith, Sabrina Cristofaro, Erin L. Heinzen, Bassel Abou-Khalil, Michael P. Epstein, Douglas E. Crompton, Eileen P.G. Vining, Kevin McKenna, Steven Petrou, Anu Venkat, Eric H. Kossoff, Gretchen Von Allmen, Sheryl R. Haut, Ruben Kuzniecky, Juliann M. Paolicchi, Colin A Ellis, Rani K. Singh, Simon Glynn, Daniel H. Lowenstein, Liu Lin Thio, Lynette G. Sadleir, Rebecca Loeb, Norman Delanty, Terence J. O'Brien, Paul V. Motika, Peter Widdess-Walsh, Sara Kivity, Gregory D. Cascino, Slavé Petrovski, Ruth Ottman, Micheline Gravel, Andrew S. Allen, Jerry J. Shih, Ingrid E. Scheffer, Joseph I Sirven, William O. Pickrell, Tracy A. Glauser, Judith L.Z. Weisenberg, Judith Bluvstein, Zaid Afawi, Phil Smith, Kevin F. Haas, Mark McCormack, Hadassa Goldberg-Stern, Sarah Paterson, Melodie R. Winawer, Mark I. Rees, Saul A. Mullen, Patrick Cossette, and Rhys H. Thomas
Subjects: Male, 0301 basic medicine, Concordance, Electroencephalography, Article, 03 medical and health sciences, Epilepsy, 0302 clinical medicine, medicine, Humans, Medical history, Generalized epilepsy, medicine.diagnostic_test, Seizure types, business.industry, Family aggregation, medicine.disease, Latent class model, Pedigree, Phenotype, 030104 developmental biology, Neurology, Latent Class Analysis, Female, Neurology (clinical), business, Epileptic Syndromes, 030217 neurology & neurosurgery, Clinical psychology
Abstract: OBJECTIVE: Classification of epilepsy into types and subtypes is important for both clinical care and research into underlying disease mechanisms. A quantitative, data-driven approach may augment traditional electroclinical classification and shed new light on existing classification frameworks. METHODS: We used latent class analysis, a statistical method that assigns subjects into groups called latent classes based on phenotypic elements, to classify individuals with common familial epilepsies from the Epi4K Multiplex Families study. Phenotypic elements included seizure types, seizure symptoms, and other elements of the medical history. We compared class assignments to traditional electroclinical classifications and assessed familial aggregation of latent classes. RESULTS: A total of 1120 subjects with epilepsy were assigned to five latent classes. Classes 1 and 2 contained subjects with generalized epilepsy, largely reflecting the distinction between absence epilepsies and younger onset (class 1) versus myoclonic epilepsies and older onset (class 2). Classes 3 and 4 contained subjects with focal epilepsies, and in contrast to classes 1 and 2, these did not adhere as closely to clinically defined focal epilepsy subtypes. Class 5 contained nearly all subjects with febrile seizures plus or unknown epilepsy type, as well as a few subjects with generalized epilepsy and a few with focal epilepsy. Family concordance of latent classes was similar to or greater than concordance of clinically defined epilepsy types. SIGNIFICANCE: Quantitative classification of epilepsy has the potential to augment traditional electroclinical classification by (1) combining some syndromes into a single class, (2) splitting some syndromes into different classes, (3) helping to classify subjects who could not be classified clinically, and (4) defining the boundaries of clinically defined classifications. This approach can guide future research, including molecular genetic studies, by identifying homogeneous sets of individuals that may share underlying disease mechanisms.
Published: 2019

26. Missense Variants in the Histone Acetyltransferase Complex Component Gene TRRAP Cause Autism and Syndromic Intellectual Disability

Author: Philippe M. Campeau, Katherine Agre, Vernon R. Sutton, Kirsty McWalter, Bertrand Isidor, Øystein L. Holla, Anna Lehman, Megha Desai, Jonathan Berg, Stéphane Bézieau, Rolph Pfundt, Jennifer Tarpinian, Jennifer B. Humberson, Holly A.F. Stessman, Madeleine R. Geisheker, Emma Bedoukian, Shalini N. Jhangiani, Marine I. Murphree, Annapurna Poduri, Anne-Sophie Denommé-Pichon, Christian Gilissen, Yaping Yang, Eliane Beauregard-Lacroix, Claude Férec, Francesca Filippini, Anne Guimier, Daryl A. Scott, Stephen Sanders, Julie C. Sapp, Ralitza H. Gavrilova, Slavé Petrovski, Ann Nordgren, Sylvia Redon, Ernie M.H.F. Bongers, Shelagh Joss, Jill A. Rosenfeld, Wallid Deb, Ingrid M. Wentzensen, Usha Kini, Vandana Shashi, Mindy H. Li, Stanislas Lyonnet, Thomas Garcia, Øyvind L. Busk, Christoffer Nellåker, Amber Begtrup, Brigitte Gilbert-Dussardier, Thomas Besnard, Francois V. Bolduc, Patrick R. Blackburn, Justine Rousseau, Frédéric Bilan, Eric W. Klee, Christopher T. Gordon, Pavel N. Pichurin, Peggy Kulch, Kevin P. Lally, Laurie Robak, Arnaud Picard, Kristian Tveten, Meredith Park, Sébastien Küry, Jaya Punetha, Moira Blyth, Asbjørg Stray-Pedersen, Jacqueline Harris, Erin L. Heinzen, Nicholas Stong, Cara M. Skraban, Julie S. Cohen, Aida Telegrafi, Xenia Latypova, Zeynep Coban Akdemir, Jacob Zyskind, Caitlin Troyer, Xiang-Jiao Yang, Tuula Rinne, Leslie G. Biesecker, Jennifer E. Posey, Kyle Retterer, Jeanne Amiel, Rui Xiao, Magnus Nordenskjöld, Tammie Dewan, Jennifer A. Sullivan, Charlotte von der Lippe, Evan E. Eichler, Anna Lindstrand, Dominique Bonneau, Yuri A. Zarate, Elaine H. Zackai, Fayth M. Kalb, Daniel H. Lowenstein, Shiri Avni, Benjamin Cogné, Jennifer J. Johnston, Kerri H. Whitlock, Catherine Shain, Séverine Audebert-Bellanger, Malin Kvarnung, Oana Caluseriu, David Goldstein, Annick Toutain, Andres Hernandez-Garcia, Brina Daniels, Sophie Ehresmann, James R. Lupski, Julie McGaughran, Ashley H Ebanks, Kévin Uguen, Marine Legendre, Sylvie Odent, Richard Redon, Erica H. Gerkes, Xiaofei Song, unité de recherche de l'institut du thorax UMR1087 UMR6291 (ITX), Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre hospitalier universitaire de Nantes (CHU Nantes), CHU Sainte Justine [Montréal], Université du Québec à Montréal = University of Québec in Montréal (UQAM), University of Oxford [Oxford], GeneDx [Gaithersburg, MD, USA], Mayo Clinic [Rochester], University of California [San Francisco] (UCSF), University of California, Génétique, génomique fonctionnelle et biotechnologies (UMR 1078) (GGB), Institut Brestois Santé Agro Matière (IBSAM), Université de Brest (UBO)-Université de Brest (UBO)-EFS-Institut National de la Santé et de la Recherche Médicale (INSERM), Etablissement Français du Sang Bretagne, EFS, Hôpital de la Cavale Blanche - CHRU Brest (CHU - BREST ), Johns Hopkins University School of Medicine [Baltimore], Kennedy Krieger Institute [Baltimore], Chapel Allerton Hospital, University of British Columbia (UBC), University of Dundee, Rush University Medical Center [Chicago], Oxford University Hospitals NHS Trust, Queen Elizabeth University Hospital (Glasgow), Trondheim University, Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), University of Virginia [Charlottesville], Texas Children's Hospital [Houston, USA], Baylor College of Medicine (BCM), Baylor University, University of Pennsylvania [Philadelphia], National Human Genome Research Institute (NHGRI), Harvard Medical School [Boston] (HMS), Karolinska University Hospital [Stockholm], Duke University Medical Center, University of Groningen [Groningen], University of Arkansas for Medical Sciences (UAMS), McGovern Medical School [Houston, Texas], The University of Texas Health Science Center at Houston (UTHealth), Phoenix Children's Hospital, Columbia University [New York], University of Southern Queensland (USQ), Telemark Hospital Trust [Skien, Norway], University of Washington [Seattle], Oslo University Hospital [Oslo], Children’s Hospital of Philadelphia (CHOP ), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Radboud University Medical Center [Nijmegen], Ann & Robert H. Lurie Children's Hospital of Chicago, Imagerie et cerveau (iBrain - Inserm U1253 - UNIV Tours ), Université de Tours-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Trousseau [Tours], Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), Institut de Génétique et Développement de Rennes (IGDR), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), CHU Pontchaillou [Rennes], Centre de référence Maladies Rares CLAD-Ouest [Rennes], Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM), Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Centre hospitalier universitaire de Poitiers (CHU Poitiers), University of Alberta, Boston Children's Hospital, McGill University Health Center [Montreal] (MUHC), Hôpital Morvan - CHRU de Brest (CHU - BREST ), Creighton University Medical School [Omaha, NE, USA], Howard Hughes Medical Institute [Boston] (HHMI), Howard Hughes Medical Institute (HHMI)-Harvard Medical School [Boston] (HMS), National Institute of Neurological Disorders and Stroke, K08 HG008986, National Human Genome Research Institute, BC Children’s Hospital Foundation, Genome British Columbia, Fonds de Recherche du Québec - Santé, Canadian Institutes of Health Research, Center for Individualized Medicine, Mayo Clinic, Health Regional Agency from Poitou-Charentes, French Ministry of Health, RC14_0107, HUGODIMS, NS053998, The Epilepsy Phenome/Genome Project, NS077303, Epi4K, Duke Genome Sequencing Clinic, NINDS R35 NS105078, National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health and Human Development, HG200328 12, intramural research program of the NHGRI, Dart NeuroScience, Kids Brain Health Network, Mining for Miracles, UM1 HG006542, National Heart, Lung, and Blood Institute, CIM Investigative and Functional Genomics Program, R01MH101221, National Institute of Mental Health, Unité de recherche de l'institut du thorax (ITX-lab), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN), University of Oxford, University of California [San Francisco] (UC San Francisco), University of California (UC), EFS-Université de Brest (UBO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Brestois Santé Agro Matière (IBSAM), Université de Brest (UBO), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), University of Virginia, University of Pennsylvania, Université de Tours (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), 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 ), MitoVasc - Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), CCSD, Accord Elsevier, Faculteit Medische Wetenschappen/UMCG, Université de Rennes 1 (UR1), and 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 )
Subjects: CHROMATIN, Male, 0301 basic medicine, Autism, Sequence Homology, [SDV.GEN] Life Sciences [q-bio]/Genetics, Medical and Health Sciences, 0302 clinical medicine, SCHIZOPHRENIA, Gene expression, 2.1 Biological and endogenous factors, Missense mutation, Aetiology, Child, de novo variants, Genetics (clinical), Pediatric, Genetics & Heredity, Genetics, biology, neurodevelopmental disorders, histone acetylation, Adaptor Proteins, Nuclear Proteins, Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6], Syndrome, Biological Sciences, Prognosis, Phenotype, Chromatin, Mental Health, Histone, intellectual disability, Child, Preschool, Female, REGULATOR, congenital malformations, Rare cancers Radboud Institute for Health Sciences [Radboudumc 9], BRAIN-DEVELOPMENT, Adult, Adolescent, Histone acetyltransferase complex, Intellectual and Developmental Disabilities (IDD), Mutation, Missense, Deciphering Developmental Disorders study, autism spectrum disorder, KAT6B, RNAI SCREEN, Young Adult, 03 medical and health sciences, CAUSES Study, Rare Diseases, Intellectual Disability, Report, COFACTOR, medicine, RUBINSTEIN-TAYBI-SYNDROME, Humans, Amino Acid Sequence, Autistic Disorder, Preschool, Gene, Genetic Association Studies, Adaptor Proteins, Signal Transducing, [SDV.GEN]Life Sciences [q-bio]/Genetics, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Rubinstein–Taybi syndrome, Signal Transducing, Neurosciences, Infant, medicine.disease, TRRAP, Brain Disorders, SELF-RENEWAL, 030104 developmental biology, DE-NOVO MUTATIONS, Mutation, biology.protein, Missense, 030217 neurology & neurosurgery
Abstract: Contains fulltext : 202928.pdf (Publisher’s version ) (Open Access) Acetylation of the lysine residues in histones and other DNA-binding proteins plays a major role in regulation of eukaryotic gene expression. This process is controlled by histone acetyltransferases (HATs/KATs) found in multiprotein complexes that are recruited to chromatin by the scaffolding subunit transformation/transcription domain-associated protein (TRRAP). TRRAP is evolutionarily conserved and is among the top five genes intolerant to missense variation. Through an international collaboration, 17 distinct de novo or apparently de novo variants were identified in TRRAP in 24 individuals. A strong genotype-phenotype correlation was observed with two distinct clinical spectra. The first is a complex, multi-systemic syndrome associated with various malformations of the brain, heart, kidneys, and genitourinary system and characterized by a wide range of intellectual functioning; a number of affected individuals have intellectual disability (ID) and markedly impaired basic life functions. Individuals with this phenotype had missense variants clustering around the c.3127G>A p.(Ala1043Thr) variant identified in five individuals. The second spectrum manifested with autism spectrum disorder (ASD) and/or ID and epilepsy. Facial dysmorphism was seen in both groups and included upslanted palpebral fissures, epicanthus, telecanthus, a wide nasal bridge and ridge, a broad and smooth philtrum, and a thin upper lip. RNA sequencing analysis of skin fibroblasts derived from affected individuals skin fibroblasts showed significant changes in the expression of several genes implicated in neuronal function and ion transport. Thus, we describe here the clinical spectrum associated with TRRAP pathogenic missense variants, and we suggest a genotype-phenotype correlation useful for clinical evaluation of the pathogenicity of the variants.
Published: 2019

27. Alternating hemiplegia of childhood: evolution over time and mouse model corroboration

Author: Milton Pratt, Julie Uchitel, Blaire Rikard, Linh Tran, Joan Jasien, Rosaria Vavassori, Carmen Fons, Elisa De Grandis, Keri Wallace, Alexis Arzimanoglou, Isabella Cocco, Erin L. Heinzen, Lyndsey Prange, Eleni Panagiotakaki, Maria T Papadopoulou, Mohamad A. Mikati, Laura Caligiuri, David Goldstein, Arsen S. Hunanyan, Rebecca Moré, Tavis Abrahamsen, and Aikaterini Vezyroglou
Subjects: Pediatrics, medicine.medical_specialty, Gross motor skill, Disease, Electroencephalography, Neurodevelopmental disorder, ATP1A3, Intellectual disability, disability, Mashlool D801N mouse, medicine, medicine.diagnostic_test, AcademicSubjects/SCI01870, business.industry, Alternating hemiplegia of childhood, General Engineering, medicine.disease, disability, Cohort, alternating hemiplegia of childhood, progression, Original Article, AcademicSubjects/MED00310, Mashlool D801N mouse, business
Abstract: Alternating hemiplegia of childhood is a rare neurodevelopmental disorder caused by ATP1A3 mutations. Some evidence for disease progression exists, but there are few systematic analyses. Here, we evaluate alternating hemiplegia of childhood progression in humans and in the D801N knock-in alternating hemiplegia of childhood mouse, Mashlool, model. This study performed an ambidirectional (prospective and retrospective data) analysis of an alternating hemiplegia of childhood patient cohort (n = 42, age 10.24 ± 1.48 years) seen at one US centre. To investigate potential disease progression, we used linear mixed effects models incorporating early and subsequent visits, and Wilcoxon Signed Rank test comparing first and last visits. Potential early-life clinical predictors were determined via multivariable regression. We also compared EEG background at first encounter and at last follow-up. We then performed a retrospective confirmation study on a multicentre cohort of alternating hemiplegia of childhood patients from France (n = 52). To investigate disease progression in the Mashlool mouse, we performed behavioural testing on a cohort of Mashlool- mice at prepubescent and adult ages (n = 11). Results: US patients, over time, demonstrated mild worsening of non-paroxysmal disability index scores, but not of paroxysmal disability index scores. Increasing age was a predictor of worse scores: P, Uchitel et al. found, in Alternating Hemiplegia of Childhood patients, that over time there is: (i) Mild worsening of non-paroxysmal neurological disability, correlating with the degree of initial (, Graphical Abstract Graphical Abstract
Published: 2021

28. 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

29. 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

30. Analysis of shared common genetic risk between amyotrophic lateral sclerosis and epilepsy

Author: Schijven, D., Stevelink, R., Mccormack, M., van Rheenen, W., Luykx, J. J., Koeleman, B. P. C., Veldink, J. H., Aleksey, Shatunov, Mclaughlin, Russell L., van der Spek, Rick A. A., Alfredo, Iacoangeli, Kenna, Kevin P., van Eijk, Kristel R., Nicola, Ticozzi, Boris, Rogelj, Katarina, Vrabec, Metka, Ravnik-Glavač, Blaž, Koritnik, Janez, Zidar, Lea, Leonardis, Leja Dolenc Grošelj, Stéphanie, Millecamps, François, Salachas, Vincent, Meininger, Mamede de Carvalho, Susana, Pinto, Marta, Gromicho, Ana, Pronto-Laborinho, Mora, Jesus S., Ricardo, Rojas-García, Meraida, Polak, Siddharthan, Chandran, Shuna, Colville, Robert, Swingler, Morrison, Karen E., Shaw, Pamela J., John, Hardy, Orrell, Richard W., Alan, Pittman, Katie, Sidle, Pietro, Fratta, Andrea, Malaspina, Simon, Topp, Susanne, Petri, Susanna, Abdulla, Carsten, Drepper, Michael, Sendtner, Thomas, Meyer, Ophoff, Roel A., Staats, Kim A., Martina, Wiedau-Pazos, Catherine, Lomen-Hoerth, Van Deerlin, Vivianna M., Trojanowski, John Q., Lauren, Elman, Leo, Mccluskey, Nazli Basak, A., Thomas, Meitinger, Peter, Lichtner, Milena, Blagojevic-Radivojkov, Andres, Christian R., Gilbert, Bensimon, Bernhard, Landwehrmeyer, Alexis, Brice, Payan, Christine A. M., Safaa, Saker-Delye, Alexandra, Dürr, Wood, Nicholas W., Lukas, Tittmann, Wolfgang, Lieb, Andre, Franke, Marcella, Rietschel, Sven, Cichon, Nöthen, Markus M., Philippe, Amouyel, Christophe, Tzourio, Jean-François, Dartigues, Uitterlinden, Andre G., Fernando, Rivadeneira, Karol, Estrada, Albert, Hofman, Charles, Curtis, van der Kooi, Anneke J., Markus, Weber, Shaw, Christopher E., Smith, Bradley N., Daisy, Sproviero, Cristina, Cereda, Mauro, Ceroni, Luca, Diamanti, Roberto Del Bo, Stefania, Corti, Comi, Giacomo P., Sandra, D'Alfonso, Lucia, Corrado, Bertolin, Cinzia, Soraru', Gianni, Letizia, Mazzini, Viviana, Pensato, Cinzia, Gellera, Cinzia, Tiloca, Antonia, Ratti, Andrea, Calvo, Cristina, Moglia, Maura, Brunetti, Simona, Arcuti, Rosa, Capozzo, Chiara, Zecca, Christian, Lunetta, Silvana, Penco, Nilo, Riva, Alessandro, Padovani, Massimiliano, Filosto, Ian, Blair, Nicholson, Garth A., Rowe, Dominic B., Roger, Pamphlett, Kiernan, Matthew C., Julian, Grosskreutz, Witte, Otto W., Robert, Steinbach, Tino, Prell, Beatrice, Stubendorff, Ingo, Kurth, Hübner, Christian A., Nigel Leigh, P., Federico, Casale, Adriano, Chio, Ettore, Beghi, Elisabetta, Pupillo, Rosanna, Tortelli, Giancarlo, Logroscino, John, Powell, Ludolph, Albert C., Weishaupt, Jochen H., Wim, Robberecht, Philip Van Damme, Brown, Robert H., Glass, Jonathan D., Landers, John E., Orla, Hardiman, Andersen, Peter M., Philippe, Corcia, Patrick, Vourc'H, Vincenzo, Silani, van Es, Michael A., Jeroen Pasterkamp, R., Lewis, Cathryn M., Gerome, Breen, Ammar, Al-Chalabi, van den Berg, Leonard H., Veldink, Jan H., Daniela, Calini, Isabella, Fogh, Barbara, Castellotti, Franco, Taroni, Stella, Gagliardi, Giacomo, Comi, Sandra, D’Alfonso, Pegoraro, Elena, Giorgia, Querin, Francesca, Gerardi, Fabrizio, Rinaldi, Maria Sofia Cotelli, Luca, Chiveri, Maria Cristina Guaita, Patrizia, Perrone, Giancarlo, Comi, Carlo, Ferrarese, Lucio, Tremolizzo, Marialuisa, Delodovici, Giorgio, Bono, Stefania, Cammarosano, Antonio, Canosa, Dario, Cocito, Leonardo, Lopiano, Luca, Durelli, Bruno, Ferrero, Antonio, Bertolotto, Alessandro, Mauro, Luca, Pradotto, Roberto, Cantello, Enrica, Bersano, Dario, Giobbe, Maurizio, Gionco, Daniela, Leotta, Lucia, Appendino, Cavallo, Cavallo, Enrico, Odddenino, Claudio, Geda, Fabio, Poglio, Paola, Santimaria, Umberto, Massazza, Antonio, Villani, Roberto, Conti, Fabrizio, Pisano, Mario, Palermo, Franco, Vergnano, Paolo, Provera, Maria Teresa Penza, Marco, Aguggia, Nicoletta Di Vito, Piero, Meineri, Ilaria, Pastore, Paolo, Ghiglione, Danilo, Seliak, Nicola, Launaro, Giovanni, Astegiano, Bottacchi, Edo, Isabella Laura Simone, Stefano, Zoccolella, Michele, Zarrelli, Franco, Apollo, William, Camu, Jean Sebastien Hulot, Francois, Viallet, Philippe, Couratier, David, Maltete, Christine, Tranchant, Marie, Vidailhet, Bassel, Abou-Khalil, Pauls, Auce, Andreja, Avbersek, Melanie, Bahlo, David, J Balding, Thomas, Bast, Larry, Baum, Albert, J Becker, Felicitas, Becker, Bianca, Berghuis, Samuel, F Berkovic, Katja, E Boysen, Jonathan, P Bradfield, Lawrence, C Brody, Russell, J Buono, Ellen, Campbell, Gregory, D Cascino, Claudia, B Catarino, Gianpiero, L Cavalleri, Stacey, S Cherny, Krishna, Chinthapalli, Alison, J Coffey, Alastair, Compston, Antonietta, Coppola, Patrick, Cossette, John, J Craig, Gerrit-Jan de Haan, Peter De Jonghe, Carolien G, F de Kovel, Norman, Delanty, Chantal, Depondt, Orrin, Devinsky, Dennis, J Dlugos, Colin, P Doherty, Christian, E Elger, Johan, G Eriksson, Thomas, N Ferraro, Martha, Feucht, Ben, Francis, Jacqueline, A French, Saskia, Freytag, Verena, Gaus, Eric, B Geller, Christian, Gieger, Tracy, Glauser, Simon, Glynn, David, B Goldstein, Hongsheng, Gui, Youling, Guo, Kevin, F Haas, Hakon, Hakonarson, Kerstin, Hallmann, Sheryl, Haut, Erin, L Heinzen, Ingo, Helbig, Christian, Hengsbach, Helle, Hjalgrim, Michele, Iacomino, Andrés, Ingason, Michael, R Johnson, Reetta, Kälviäinen, Anne-Mari, Kantanen, Dalia, Kasperavičiūte, Dorothee Kasteleijn-Nolst Trenite, Heidi, E Kirsch, Robert, C Knowlton, Bobby P, C Koeleman, Roland, Krause, Martin, Krenn, Wolfram, S Kunz, Ruben, Kuzniecky, Patrick, Kwan, Dennis, Lal, Yu-Lung, Lau, Anna-Elina, Lehesjoki, Holger, Lerche, Costin, Leu, Dick, Lindhout, Warren, D Lo, Iscia, Lopes-Cendes, Daniel, H Lowenstein, Alberto, Malovini, Anthony, G Marson, Thomas, Mayer, Mark, Mccormack, James, L Mills, Nasir, Mirza, Martina, Moerzinger, Rikke, S Møller, Anne, M Molloy, Hiltrud, Muhle, Mark, Newton, Ping-Wing, Ng, Markus, M Nöthen, Peter, Nürnberg, Terence, J O’Brien, Karen, L Oliver, Aarno, Palotie, Faith, Pangilinan, Sarah, Peter, Slavé, Petrovski, Annapurna, Poduri, Michael, Privitera, Rodney, Radtke, Sarah, Rau, Philipp, S Reif, Eva, M Reinthaler, Felix, Rosenow, Josemir, W Sander, Thomas, Sander, Theresa, Scattergood, Steven, C Schachter, Christoph, J Schankin, Ingrid, E Scheffer, Bettina, Schmitz, Susanne, Schoch, Pak, C Sham, Jerry, J Shih, Graeme, J Sills, Sanjay, M Sisodiya, Lisa, Slattery, Alexander, Smith, David, F Smith, Michael, C Smith, Philip, E Smith, Anja C, M Sonsma, Doug, Speed, Michael, R Sperling, Bernhard, J Steinhoff, Ulrich, Stephani, Remi, Stevelink, Konstantin, Strauch, Pasquale, Striano, Hans, Stroink, Rainer, Surges, K Meng Tan, Liu Lin Thio, G Neil Thomas, Marian, Todaro, Rossana, Tozzi, Maria, S Vari, Eileen P, G Vining, Frank, Visscher, Sarah von Spiczak, Nicole, M Walley, Yvonne, G Weber, Zhi, Wei, Judith, Weisenberg, Christopher, D Whelan, Peter, Widdess-Walsh, Markus, Wolff, Stefan, Wolking, Wanling, Yang, Federico, Zara, Fritz, Zimprich, Project MinE ALS GWAS Consortium, International League Against Epilepsy Consortium on Complex Epilepsies, Department of Medical and Clinical Genetics, Centre of Excellence in Complex Disease Genetics, Aarno Palotie / Principal Investigator, Institute for Molecular Medicine Finland, Genomics of Neurological and Neuropsychiatric Disorders, Clinicum, Johan Eriksson / Principal Investigator, Department of General Practice and Primary Health Care, and HUS Helsinki and Uusimaa Hospital District
Subjects: Risk, 0301 basic medicine, Aging, Genetic correlation, Geriatrics & Gerontology, education, Genome-wide association study, Biology, ALS, Epilepsy, Amyotrophic Lateral Sclerosis, Gene Frequency, Humans, Genetic Variation, Genome-Wide Association Study, Negative Results, Article, 3124 Neurology and psychiatry, 03 medical and health sciences, 0302 clinical medicine, Genetic variation, medicine, Amyotrophic lateral sclerosis, Allele frequency, Genetics, Science & Technology, Mechanism (biology), General Neuroscience, 3112 Neurosciences, Neurosciences, medicine.disease, 3. Good health, Minor allele frequency, 030104 developmental biology, Neurology (clinical), Neurosciences & Neurology, Geriatrics and Gerontology, Life Sciences & Biomedicine, 030217 neurology & neurosurgery, Developmental Biology
Abstract: Because hyper-excitability has been shown to be a shared pathophysiological mechanism, we used the latest and largest genome-wide studies in amyotrophic lateral sclerosis (n = 36,052) and epilepsy (n = 38,349) to determine genetic overlap between these conditions. First, we showed no significant genetic correlation, also when binned on minor allele frequency. Second, we confirmed the absence of polygenic overlap using genomic risk score analysis. Finally, we did not identify pleiotropic variants in meta-analyses of the 2 diseases. Our findings indicate that amyotrophic lateral sclerosis and epilepsy do not share common genetic risk, showing that hyper-excitability in both disorders has distinct origins. ispartof: NEUROBIOLOGY OF AGING vol:92 ispartof: location:United States status: published
Published: 2020

31. D-DEMØ, a distinct phenotype caused by ATP1A3 mutations

Author: Vijay Pagadala, Erin L. Heinzen, Melissa McLean, David M. Mueller, Kristin Herman, Lyndsey Prange, Raphael Schiffmann, Mohamad A. Mikati, David Goldstein, Vandana Shashi, Nicole M. Walley, Mary Moya Mendez, Arsen S. Hunanyan, and Milton Pratt
Subjects: Dystonia, Pathology, medicine.medical_specialty, business.industry, Encephalopathy, Neonatal onset, Nystagmus, medicine.disease, Hypotonia, Article, Atrophy, ATP1A3, medicine, Neurology (clinical), medicine.symptom, business, Cerebellar hypoplasia, Genetics (clinical)
Abstract: ObjectiveTo describe a phenotype caused byATP1A3mutations, which manifests as dystonia, dysmorphism of the face, encephalopathy with developmental delay, brain MRI abnormalities always including cerebellar hypoplasia, no hemiplegia (Ø) (D-DEMØ), and neonatal onset.MethodsReview and analysis of clinical and genetic data.ResultsPatients shared the above traits and had whole-exome sequencing that showed de novo variants of theATP1A3gene, predicted to be disease causing and occurring in regions of the protein critical for pump function. Patient 1 (c.1079C>G, p.Thr360Arg), an 8-year-old girl, presented on day 1 of life with episodic dystonia, complex partial seizures, and facial dysmorphism. MRI of the brain revealed cerebellar hypoplasia. Patient 2 (c.420G>T, p.Gln140His), an 18-year-old man, presented on day 1 of life with hypotonia, tremor, and facial dysmorphism. He later developed dystonia. MRI of the brain revealed cerebellar hypoplasia and, later, further cerebellar volume loss (atrophy). Patient 3 (c.974G>A, Gly325Asp), a 13-year-old girl, presented on day 1 of life with tremor, episodic dystonia, and facial dysmorphism. MRI of the brain showed severe cerebellar hypoplasia. Patient 4 (c.971A>G, p.Glu324Gly), a 14-year-old boy, presented on day 1 of life with tremor, hypotonia, dystonia, nystagmus, facial dysmorphism, and later seizures. MRI of the brain revealed moderate cerebellar hypoplasia.ConclusionsD-DEMØ represents anATP1A3-related phenotype, the observation of which should trigger investigation forATP1A3mutations. Our findings, and the presence of multiple distinctATP1A3-related phenotypes, support the possibility that there are differences in the underlying mechanisms.
Published: 2020

32. Expansion of the GRIA2 phenotypic representation: a novel de novo loss of function mutation in a case with childhood onset schizophrenia

Author: Anna, Alkelai, Shahar, Shohat, Lior, Greenbaum, Tanya, Schechter, Benjamin, Draiman, Eti, Chitrit-Raveh, Shlomit, Rienstein, Neha, Dagaonkar, Daniel, Hughes, Vimla S, Aggarwal, Erin L, Heinzen, Sagiv, Shifman, David B, Goldstein, and Yoav, Kohn
Subjects: Aggression, Aphasia, Broca, Obsessive-Compulsive Disorder, Young Adult, Attention Deficit Disorder with Hyperactivity, Learning Disabilities, Loss of Function Mutation, Exome Sequencing, Humans, Female, Receptors, AMPA, Anxiety, Schizophrenia, Childhood
Abstract: Childhood-onset schizophrenia (COS) is a rare form of schizophrenia with an onset before 13 years of age. There is rising evidence that genetic factors play a major role in COS etiology, yet, only a few single gene mutations have been discovered. Here we present a diagnostic whole-exome sequencing (WES) in an Israeli Jewish female with COS and additional neuropsychiatric conditions such as obsessive-compulsive disorder (OCD), anxiety, and aggressive behavior. Variant analysis revealed a de novo novel stop gained variant in GRIA2 gene (NM_000826.4: c.1522 G T (p.Glu508Ter)). GRIA2 encodes for a subunit of the AMPA sensitive glutamate receptor (GluA2) that functions as ligand-gated ion channel in the central nervous system and plays an important role in excitatory synaptic transmission. GluA2 subunit mutations are known to cause variable neurodevelopmental phenotypes including intellectual disability, autism spectrum disorder, epilepsy, and OCD. Our findings support the potential diagnostic role of WES in COS, identify GRIA2 as possible cause to a broad psychiatric phenotype that includes COS as a major manifestation and expand the previously reported GRIA2 loss of function phenotypes.
Published: 2020

33. Somatic variants in epilepsy - advancing gene discovery and disease mechanisms

Author: Erin L. Heinzen
Subjects: Genetic Markers, Cell type, Somatic cell, Computational biology, Biology, Article, 03 medical and health sciences, Epilepsy, 0302 clinical medicine, Genetics, medicine, Animals, Humans, Genetic Predisposition to Disease, Genetic Association Studies, 030304 developmental biology, 0303 health sciences, Disease mechanisms, Genetic variants, medicine.disease, Phenotype, Disease Presentation, Mutation, 030217 neurology & neurosurgery, Gene Discovery, Developmental Biology
Abstract: In the past ten years, there has been increasing recognition that cells can acquire genetic variants during cortical development that can give rise to brain malformations as well as nonlesional focal epilepsy. These often brain tissue-specific, de novo variants can result in highly variable phenotypes based on the burden of a variant in specific tissues and cells. By discovering these variants, shared pathophysiological mechanisms are being revealed between clinically distinct disorders. Beyond informing disease mechanisms, mosaic variants also offer a powerful research tool to trace cellular lineages, to study the roles of specialized cell types in disease presentation, and to establish the cell-type specific genomic consequences of a variant.
Published: 2020

34. 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

35. Development and validation of a predictive model of drug-resistant genetic generalized epilepsy

Author: Arjune Sen, Hyunmi Choi, Piero Perucca, Erin L. Heinzen, Manahil Muneeb, Gary A. Heiman, Carl W. Bazil, Chantal Depondt, Hatem Tolba, Kamil Detyniecki, Peter Crosta, Lawrence J. Hirsch, and Suzanne Thornton
Subjects: Adult, Male, Longitudinal study, Pediatrics, medicine.medical_specialty, Drug Resistant Epilepsy, Adolescent, Lamotrigine, Article, 03 medical and health sciences, Epilepsy, Young Adult, 0302 clinical medicine, medicine, Catamenial epilepsy, Humans, 030212 general & internal medicine, Longitudinal Studies, Age of Onset, Child, Models, Statistical, business.industry, Seizure types, Case-control study, Sciences bio-médicales et agricoles, medicine.disease, Case-Control Studies, Child, Preschool, Observational study, Epilepsy, Generalized, Female, Neurology (clinical), business, 030217 neurology & neurosurgery, medicine.drug
Abstract: To develop and validate a clinical prediction model for antiepileptic drug (AED)-resistant genetic generalized epilepsy (GGE)., info:eu-repo/semantics/published
Published: 2019

36. New insights into tardive dyskinesia genetics: Implementation of whole-exome sequencing approach

Author: Lior Greenbaum, Rael D. Strous, Deborah L. Levy, Arun K. Tiwari, Maria Tampakeras, Natalie Freeman, Shannon Delaney, Daniel J. Müller, Ann E. Pulver, James L. Kennedy, Erin L. Heinzen, Evan H. Baugh, Bernard Lerer, Herbert Y. Meltzer, Emma P. Peabody, Anna Alkelai, Gary Remington, Clement C. Zai, Jeffrey A. Lieberman, Alexander Teitelbaum, Aristotle N. Voineskos, Xiaolin Zhu, and Pavel Tatarskyy
Subjects: Adult, Male, Candidate gene, Dyskinesia, Drug-Induced, Population, Tardive dyskinesia, 03 medical and health sciences, Young Adult, 0302 clinical medicine, Gene Frequency, Exome Sequencing, medicine, Humans, Genetic Predisposition to Disease, Allele, education, Biological Psychiatry, Exome sequencing, Aged, Pharmacology, Genetics, education.field_of_study, business.industry, Middle Aged, medicine.disease, 030227 psychiatry, Exact test, Schizophrenia, Case-Control Studies, Female, business, Pharmacogenetics, Antipsychotic Agents
Abstract: Tardive dyskinesia (TD) is an adverse movement disorder induced by chronic treatment with antipsychotics drugs. The contribution of common genetic variants to TD susceptibility has been investigated in recent years, but with limited success. The aim of the current study was to investigate the potential contribution of rare variants to TD vulnerability. In order to identify TD risk genes, we performed whole-exome sequencing (WES) and gene-based collapsing analysis focusing on rare (allele frequency
Published: 2019

37. The copy number variation landscape of congenital anomalies of the kidney and urinary tract

Author: Adele Mitrotti, David Fasel, Nan Wu, Joanna A.E. van Wijk, Monica Bodria, Jeremiah Martino, Alejandra Perez, Marcin Tkaczyk, Loreto Gesualdo, Katarzyna Zachwieja, Marcin Zaniew, Giorgio Piaggio, Miguel Verbitsky, Brynn Levy, Virginia E. Papaioannou, Zoran Gucev, Marijan Saraga, Piotr Adamczyk, David E. Barton, Velibor Tasic, Craig S. Wong, Maria Szczepańska, Rik Westland, Valeria Manca, Jun Zhang, Alba Carrea, Fangming Lin, Robert Pawluch, Pasquale Casale, Landino Allegri, Krzysztof Kiryluk, Matthew G. Sampson, Daniele Cusi, Charlly Kao, Max Werth, Shumyle Alam, Young Ji Na, Claudia Izzi, Isabella Pisani, Mark G Dobson, Grażyna Krzemień, Giovanni Conti, Dorota Drozdz, John M Darlow, Shirlee Shril, Patricia L. Weng, Tze Y Lim, Friedhelm Hildebrandt, Monika Miklaszewska, Giuseppe Masnata, Domenico Santoro, Ana Cristina Simões-e-Silva, Byum Hee Kil, Cathy Mendelsohn, Hakon Hakonarson, Przemysław Sikora, Anna Latos-Bielenska, Simone Sanna-Cherchi, Josep M. Campistol, Anna Krakowska, Cécile Jeanpierre, Pasquale Zamboli, Débora Marques de Miranda, Hope White, Francesco Scolari, Dina Ahram, Ekaterina Batourina, Anna Materna-Kiryluk, Valentina P Capone, Eduardo A. Oliveira, Maddalena Marasa, Tomasz Jarmoliński, Jonathan Barasch, Asaf Vivante, Prem Puri, Ali G. Gharavi, Feng Zhang, Priya Krithivasan, Małgorzata Mizerska-Wasiak, Erin L. Heinzen, Maria K Borszewska-Kornacka, Lida Rodas, Bradley A. Warady, Maddalena Gigante, Agnieszka Szmigielska, Qingxue Liu, Susan L. Furth, Vladimir J Lozanovski, Gian Marco Ghiggeri, Daria Tomczyk, Amsterdam Reproduction & Development (AR&D), ACS - Microcirculation, and Paediatric Nephrology
Subjects: Male, BIOMEDICINE AND HEALTHCARE. Clinical Medical Sciences, endocrine system diseases, Kidney, 0302 clinical medicine, Copy-number variation, deletion, Urinary Tract, Obstructive uropathy, Genetics, 0303 health sciences, BIOMEDICINA I ZDRAVSTVO. Kliničke medicinske znanosti, Genomics, digeorge-syndrome, Microdeletion syndrome, 3. Good health, medicine.anatomical_structure, Female, vitamin-a, branching morphogenesis, Chromosome Deletion, candidate genes, renal replacement therapy, congenital, hereditary, and neonatal diseases and abnormalities, DNA Copy Number Variations, Urinary system, Locus (genetics), Biology, Vesicoureteral reflux, Article, 03 medical and health sciences, mental disorders, medicine, Humans, Genetic Predisposition to Disease, genomic disorders, 030304 developmental biology, Vesico-Ureteral Reflux, disease, Extramural, rare variants, medicine.disease, mutations, Urogenital Abnormalities, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract: Congenital anomalies of the kidney and urinary tract (CAKUT) are a major cause of pediatric kidney failure. We performed a genome-wide analysis of copy number variants (CNVs) in 2, 824 cases and 21, 498 controls. Affected individuals carried a significant burden of rare exonic (i.e. affecting coding regions) CNVs and were enriched for known genomic disorders (GD). Kidney anomaly (KA) cases were most enriched for exonic CNVs, encompassing GD- CNVs and novel deletions ; obstructive uropathy (OU) had a lower CNV burden and an intermediate prevalence of GD-CNVs ; vesicoureteral reflux (VUR) had the fewest GD-CNVs but was enriched for novel exonic CNVs, particularly duplications. Six loci (1q21, 4p16.1-p16.3, 16p11.2, 16p13.11, 17q12, and 22q11.2) accounted for 65% of patients with GD-CNVs. Deletions at 17q12, 4p16.1- p16.3, and 22q11.2 were specific for KA ; the 16p11.2 locus showed extensive pleiotropy. Using a multidisciplinary approach, we identified TBX6 as a driver for the CAKUT subphenotypes in the 16p11.2 microdeletion syndrome.
Published: 2019

38. 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

39. Autism and developmental disability caused by KCNQ3 gain-of-function variants

Author: Kavita Thakkar, François Rivier, Bitten Schönewolf-Greulich, Gaetan Lesca, Christine Francannet, Nicholas Stong, Sarah Weckhuysen, Vandana Shashi, Marjolaine Willems, Zeynep Tümer, David Goldstein, Daniel K. Arrington, Eric H. Kossoff, Anita E. Beck, Maria Virginia Soldovieri, Erin L. Heinzen, Edward C. Cooper, A. James Barkovich, Heather C Mefford, Francesco Miceli, Lynette G. Sadleir, Tristan T. Sands, Anna Lauritano, Amber Stocco, Ingrid E. Scheffer, Anne Marie Bisgaard, Ana Grijalvo Perez, Deepa S. Rajan, M. Roberta Cilio, Piera Nappi, Bénédicte Gérard, Sébastien Moutton, Maurizio Taglialatela, Antonio Vitobello, Jennifer A. Sullivan, UCL - SSS/IREC/PEDI - Pôle de Pédiatrie, UCL - (SLuc) Service de neurologie pédiatrique, Sands, T. T., Miceli, F., Lesca, G., Beck, A. E., Sadleir, L. G., Arrington, D. K., Schonewolf-Greulich, B., Moutton, S., Lauritano, A., Nappi, P., Soldovieri, M. V., Scheffer, I. E., Mefford, H. C., Stong, N., Heinzen, E. L., Goldstein, D. B., Perez, A. G., Kossoff, E. H., Stocco, A., Sullivan, J. A., Shashi, V., Gerard, B., Francannet, C., Bisgaard, A. -M., Tumer, Z., Willems, M., Rivier, F., Vitobello, A., Thakkar, K., Rajan, D. S., Barkovich, A. J., Weckhuysen, S., Cooper, E. C., Taglialatela, M., Cilio, M. R., Columbia University Medical Center (CUMC), Columbia University [New York], 'Federico II' University of Naples Medical School, Centre de recherche en neurosciences de Lyon (CRNL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Pediatrics, University of Washington, Seattle, WA, USA., University of Otago [Dunedin, Nouvelle-Zélande], St. Luke's Children's Hospital, Department of Paediatrics and Adolescent Medicine, 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), Department of Neuroscience, University of Naples 'Federico II,' Naples, Italy., University of Molise, Epilepsy Research Centre, University of Melbourne, University of Washington, Columbia University Irving Medical Center (CUIMC), University of California [San Francisco] (UCSF), University of California, Johns Hopkins University School of Medicine [Baltimore], INTEGRIS Baptist Medical Center, School of Irish, Celtic Studies, Irish Folklore and Linguistics, University College Dublin [Dublin] (UCD), Duke University [Durham], Service d'hématologie et immunologie, Université Paris Diderot - Paris 7 (UPD7)-AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Unité de Génétique Médicale, Hôtel-Dieu-CHU Clermont-Ferrand, Rigshospitalet [Copenhagen], Copenhagen University Hospital, Clinical genetic clinic, Département de génétique médicale, maladies rares et médecine personnalisée [CHRU Montpellier], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Physiologie & médecine expérimentale du Cœur et des Muscles [U 1046] (PhyMedExp), Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Equipe GAD (LNC - U1231), Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Santé et de la Recherche Médicale (INSERM), University of Pittsburgh School of Medicine, Pennsylvania Commonwealth System of Higher Education (PCSHE), Hospices Civils de Lyon (HCL), Centre de référence des épilepsies rares [CHU Pitié-Salpêtrière], Unité fonctionnelle d'épilepsie [CHU Pitié-Salpêtrière], Service de Neurologie [CHU Pitié-Salpêtrière], IFR70-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)-IFR70-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 Neurologie [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), University of Antwerp, Antwerp, Belgium., Baylor College of Medecine, Section of Pharmacology, Università degli studi di Napoli Federico II, University of Naples 'Federico II,', University of Louvain, MORNET, Dominique, Centre de recherche en neurosciences de Lyon - Lyon Neuroscience Research Center (CRNL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of Washington [Seattle], University of Naples Federico II = Università degli studi di Napoli Federico II, Università degli Studi del Molise = University of Molise (UNIMOL), Department of Pediatrics [Seattle], University of California [San Francisco] (UC San Francisco), University of California (UC), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Diderot - Paris 7 (UPD7), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), 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, University of Antwerp (UA), Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-IFR70-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Service de Neurologie [CHU Pitié-Salpêtrière], and Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)
Subjects: 0301 basic medicine, Male, Pediatrics, medicine.medical_specialty, Developmental Disabilities, [SDV]Life Sciences [q-bio], Encephalopathy, Electroencephalography, Protein Structure, Secondary, KCNQ3 Potassium Channel, 03 medical and health sciences, Epilepsy, Young Adult, 0302 clinical medicine, medicine, Humans, Global developmental delay, Amino Acid Sequence, Young adult, Autistic Disorder, Child, ComputingMilieux_MISCELLANEOUS, medicine.diagnostic_test, business.industry, Genetic Variation, medicine.disease, 3. Good health, [SDV] Life Sciences [q-bio], 030104 developmental biology, Clinical research, Neurology, Autism spectrum disorder, Child, Preschool, Gain of Function Mutation, Autism, Neurology (clinical), Human medicine, business, 030217 neurology & neurosurgery
Abstract: Objective Recent reports have described single individuals with neurodevelopmental disability (NDD) harboring heterozygous KCNQ3 de novo variants (DNVs). We sought to assess whether pathogenic variants in KCNQ3 cause NDD and to elucidate the associated phenotype and molecular mechanisms. Methods Patients with NDD and KCNQ3 DNVs were identified through an international collaboration. Phenotypes were characterized by clinical assessment, review of charts, electroencephalographic (EEG) recordings, and parental interview. Functional consequences of variants were analyzed in vitro by patch-clamp recording. Results Eleven patients were assessed. They had recurrent heterozygous DNVs in KCNQ3 affecting residues R230 (R230C, R230H, R230S) and R227 (R227Q). All patients exhibited global developmental delay within the first 2 years of life. Most (8/11, 73%) were nonverbal or had a few words only. All patients had autistic features, and autism spectrum disorder (ASD) was diagnosed in 5 of 11 (45%). EEGs performed before 10 years of age revealed frequent sleep-activated multifocal epileptiform discharges in 8 of 11 (73%). For 6 of 9 (67%) recorded between 1.5 and 6 years of age, spikes became near-continuous during sleep. Interestingly, most patients (9/11, 82%) did not have seizures, and no patient had seizures in the neonatal period. Voltage-clamp recordings of the mutant KCNQ3 channels revealed gain-of-function (GoF) effects. Interpretation Specific GoF variants in KCNQ3 cause NDD, ASD, and abundant sleep-activated spikes. This new phenotype contrasts both with self-limited neonatal epilepsy due to KCNQ3 partial loss of function, and with the neonatal or infantile onset epileptic encephalopathies due to KCNQ2 GoF. ANN NEUROL 2019;86:181-192
Published: 2019

40. Genome-wide mega-analysis identifies 16 loci and highlights diverse biological mechanisms in the common epilepsies

Author: Christian E. Elger, Wolfgang Lieb, Claudia B. Catarino, Pasquale Striano, Andreja Avbersek, Daniel H. Lowenstein, Philip E. M. Smith, G. Neil Thomas, Dick Lindhout, Erin L. Heinzen, Sanjay M. Sisodiya, Orrin Devinsky, Alexander R. H. Smith, Rainer Surges, Stefan Wolking, Patrick Cossette, Annapurna Poduri, Eric B. Geller, Stacey S. Cherny, Maria Stella Vari, Peter De Jonghe, Kevin Haas, Andres Ingason, Reetta Kälviäinen, Krishna Chinthapalli, Dennis Lal, Graeme J. Sills, Martina Moerzinger, Jonathan P. Bradfield, Mark R Newton, Federico Zara, Sheryl R. Haut, Warren D. Lo, Holger Lerche, Felix Rosenow, Robert C. Knowlton, Mark McCormack, Sarah Rau, Felicitas Becker, Andre Franke, Heidi E. Kirsch, Patrick Kwan, Remi Stevelink, Rodney A. Radtke, Michele Iacomino, Faith Pangilinan, Ulrich Stephani, David F. Smith, Eva M. Reinthaler, Chantal Depondt, Hiltrud Muhle, Russell J. Buono, Alison J. Coffey, Ellen Campbell, Marvin Johnson, Bernhard J. Steinhoff, Sarah von Spiczak, Yvonne G. Weber, Ping-Wing Ng, Kerstin Hallmann, Philipp S. Reif, David Goldstein, Bettina Schmitz, Antonietta Coppola, Jerry J. Shih, Karen Oliver, Anne-Mari Kantanen, Rossana Tozzi, Markus Wolff, Albert J. Becker, Anne M. Molloy, Lisa Slattery, James L. Mills, Judith L.Z. Weisenberg, Jacqueline A. French, Lawrence C. Brody, Int League Against Epilepsy Conso, Peter Widdess-Walsh, Helle Hjalgrim, Christian Hengsbach, Christoph J. Schankin, Johan G. Eriksson, Tracy A. Glauser, Yu-Lung Lau, Larry Baum, Anna-Elina Lehesjoki, Nicole M. Walley, Josemir W. Sander, Markus M. Noethen, Simon Glynn, Jennifer Jamnadas-Khoda, Thomas Bast, Susanne Schoch, Iscia Lopes-Cendes, Doug Speed, Anja C M Sonsma, John Craig, Ingo Helbig, Marian Todaro, Gregory D. Cascino, Steven C. Schachter, Fritz Zimprich, Samuel F. Berkovic, Michael Privitera, Ben Francis, Martin Krenn, Rikke S. Møller, Eileen P.G. Vining, Martha Feucht, Bobby P. C. Koeleman, Ruben Kuzniecky, Christian Gieger, K. Meng Tan, Dalia Kasperaviciute, Pauls Auce, Gianpiero L. Cavalleri, Melanie Bahlo, Zhi Wei, Nasir Mirza, David J. Balding, Mike Smith, Liu Lin Thio, Alastair Compston, Katja E. Boysen, Gerrit-Jan de Haan, Hongsheng Gui, Hakon Hakonarson, Christopher D. Whelan, Colin P. Doherty, Youling Guo, Aarno Palotie, Wolfram S. Kunz, Slavé Petrovski, Thomas Sander, Frank Visscher, Bianca Berghuis, Costin Leu, Verena Gaus, Dennis J. Dlugos, Ingrid E. Scheffer, Alberto Malovini, Konstantin Strauch, Wanling Yang, Saskia Freytag, H. Stroink, Pak C. Sham, Norman Delanty, Terence J. O'Brien, Carolien G.F. de Kovel, Thomas U. Mayer, Anthony G Marson, Bassel Abou-Khalil, Thomas N. Ferraro, Dorothée G.A. Kasteleijn-Nolst Trenité, Roland Krause, Sarah Peter, Peter Nuernberg, Theresa Scattergood, Michael R. Sperling, Johan Eriksson / Principal Investigator, Department of General Practice and Primary Health Care, Clinicum, Department of Medical and Clinical Genetics, Medicum, Centre of Excellence in Complex Disease Genetics, Aarno Palotie / Principal Investigator, Institute for Molecular Medicine Finland, Genomics of Neurological and Neuropsychiatric Disorders, Int League Against Epilepsy Conso, Abou-Khalil, Bassel, Auce, Paul, Avbersek, Andreja, Bahlo, Melanie, J Balding, David, Bast, Thoma, Baum, Larry, J Becker, Albert, Becker, Felicita, Berghuis, Bianca, F Berkovic, Samuel, E Boysen, Katja, P Bradfield, Jonathan, C Brody, Lawrence, J Buono, Russell, Campbell, Ellen, D Cascino, Gregory, B Catarino, Claudia, L Cavalleri, Gianpiero, S Cherny, Stacey, Chinthapalli, Krishna, J Coffey, Alison, Compston, Alastair, Coppola, Antonietta, Cossette, Patrick, J Craig, John, de Haan, Gerrit-Jan, De Jonghe, Peter, F de Kovel, Carolien G, Delanty, Norman, Depondt, Chantal, Devinsky, Orrin, J Dlugos, Denni, P Doherty, Colin, E Elger, Christian, G Eriksson, Johan, N Ferraro, Thoma, Feucht, Martha, Francis, Ben, Franke, Andre, A French, Jacqueline, Freytag, Saskia, Gaus, Verena, B Geller, Eric, Gieger, Christian, Glauser, Tracy, Glynn, Simon, B Goldstein, David, Gui, Hongsheng, Guo, Youling, F Haas, Kevin, Hakonarson, Hakon, Hallmann, Kerstin, Haut, Sheryl, L Heinzen, Erin, Helbig, Ingo, Hengsbach, Christian, Hjalgrim, Helle, Iacomino, Michele, Ingason, André, Jamnadas-Khoda, Jennifer, R Johnson, Michael, Kälviäinen, Reetta, Kantanen, Anne-Mari, Kasperavičiūte, Dalia, Kasteleijn-Nolst Trenite, Dorothee, E Kirsch, Heidi, C Knowlton, Robert, C Koeleman, Bobby P, Krause, Roland, Krenn, Martin, S Kunz, Wolfram, Kuzniecky, Ruben, Kwan, Patrick, Lal, Denni, Lau, Yu-Lung, Lehesjoki, Anna-Elina, Lerche, Holger, Leu, Costin, Lieb, Wolfgang, Lindhout, Dick, D Lo, Warren, Lopes-Cendes, Iscia, H Lowenstein, Daniel, Malovini, Alberto, G Marson, Anthony, Mayer, Thoma, Mccormack, Mark, L Mills, Jame, Mirza, Nasir, Moerzinger, Martina, S Møller, Rikke, M Molloy, Anne, Muhle, Hiltrud, Newton, Mark, Ng, Ping-Wing, M Nöthen, Marku, Nürnberg, Peter, J O'Brien, Terence, L Oliver, Karen, Palotie, Aarno, Pangilinan, Faith, Peter, Sarah, Petrovski, Slavé, Poduri, Annapurna, Privitera, Michael, Radtke, Rodney, Rau, Sarah, S Reif, Philipp, M Reinthaler, Eva, Rosenow, Felix, W Sander, Josemir, Sander, Thoma, Scattergood, Theresa, C Schachter, Steven, J Schankin, Christoph, E Scheffer, Ingrid, Schmitz, Bettina, Schoch, Susanne, C Sham, Pak, J Shih, Jerry, J Sills, Graeme, M Sisodiya, Sanjay, Slattery, Lisa, Smith, Alexander, F Smith, David, C Smith, Michael, E Smith, Philip, M Sonsma, Anja C, Speed, Doug, R Sperling, Michael, J Steinhoff, Bernhard, Stephani, Ulrich, Stevelink, Remi, Strauch, Konstantin, Striano, Pasquale, Stroink, Han, Surges, Rainer, Meng Tan, K, Lin Thio, Liu, Neil Thomas, G, Todaro, Marian, Tozzi, Rossana, S Vari, Maria, G Vining, Eileen P, Visscher, Frank, von Spiczak, Sarah, M Walley, Nicole, G Weber, Yvonne, Wei, Zhi, Weisenberg, Judith, D Whelan, Christopher, Widdess-Walsh, Peter, Wolff, Marku, Wolking, Stefan, Yang, Wanling, Zara, Federico, Zimprich, Fritz, Wellcome Trust, GlaxoSmithKline Services Unlimited, Commission of the European Communities, Medical Research Council (MRC), and Imperial College Healthcare NHS Trust- BRC Funding
Subjects: 0301 basic medicine, Linkage disequilibrium, LD SCORE REGRESSION, Neurology [D14] [Human health sciences], General Physics and Astronomy, Genome-wide association study, ILAE COMMISSION, Neurodegenerative, Genome, Linkage Disequilibrium, Epilepsy, Gene Frequency, Missing heritability problem, 2.1 Biological and endogenous factors, Aetiology, lcsh:Science, International League Against Epilepsy Consortium on Complex Epilepsies, Multidisciplinary, Genetic Predisposition to Disease/genetics, Chromosome Mapping, ASSOCIATION, Epilepsy/classification, Single Nucleotide, ABSENCE, 3. Good health, Technologie de l'environnement, contrôle de la pollution, SNP HERITABILITY, Neurological, Genome-Wide Association Study/methods, Case-Control Studie, Engineering sciences. Technology, Human, Biotechnology, EXPRESSION, SUSCEPTIBILITY LOCI, Genotype, Science, Quantitative Trait Loci, 610 Medicine & health, Computational biology, Biology, Quantitative trait locus, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, Article, GENETIC ARCHITECTURE, 03 medical and health sciences, MD Multidisciplinary, medicine, Genetics, SNP, Chimie, FRONTAL-LOBE, Humans, Genetic Predisposition to Disease, Polymorphism, METAANALYSIS, Neurologie [D14] [Sciences de la santé humaine], Physique, Human Genome, Neurosciences, General Chemistry, Astronomie, medicine.disease, Genetic architecture, Brain Disorders, 030104 developmental biology, Gene Expression Regulation, Case-Control Studies, epilepsy, lcsh:Q, 3111 Biomedicine, Quantitative Trait Loci/genetics, Genome-Wide Association Study
Abstract: The epilepsies affect around 65 million people worldwide and have a substantial missing heritability component. We report a genome-wide mega-analysis involving 15,212 individuals with epilepsy and 29,677 controls, which reveals 16 genome-wide significant loci, of which 11 are novel. Using various prioritization criteria, we pinpoint the 21 most likely epilepsy genes at these loci, with the majority in genetic generalized epilepsies. These genes have diverse biological functions, including coding for ion-channel subunits, transcription factors and a vitamin-B6 metabolism enzyme. Converging evidence shows that the common variants associated with epilepsy play a role in epigenetic regulation of gene expression in the brain. The results show an enrichment for monogenic epilepsy genes as well as known targets of antiepileptic drugs. Using SNP-based heritability analyses we disentangle both the unique and overlapping genetic basis to seven different epilepsy subtypes. Together, these findings provide leads for epilepsy therapies based on underlying pathophysiology., SCOPUS: ar.j, info:eu-repo/semantics/published
Published: 2018

41. Mutations of the Sonic Hedgehog Pathway Underlie Hypothalamic Hamartoma with Gelastic Epilepsy

Author: Nigel C. Jones, David Goldstein, Michael S. Hildebrand, John A. Damiano, John F. Kerrigan, Ezgi Ozturk, Benjamin W. Darbro, Erin L. Heinzen, Lynette G. Sadleir, Nicole G. Griffin, Heather J. Major, Rosemary Burgess, Jeremy L. Freeman, Richard J. Leventer, Andrew S. Allen, A. Simon Harvey, Ingrid E. Scheffer, Samuel F. Berkovic, and Elisa J. Cops
Subjects: Male, 0301 basic medicine, Candidate gene, animal structures, Hamartoma, Kruppel-Like Transcription Factors, Loss of Heterozygosity, Nerve Tissue Proteins, Zinc Finger Protein Gli2, 03 medical and health sciences, 0302 clinical medicine, Hypothalamic hamartoma, Zinc Finger Protein Gli3, Report, GLI2, GLI3, Genetics, Humans, Exome, Hedgehog Proteins, Genetics(clinical), Sonic hedgehog, Genetics (clinical), Cyclic AMP-Dependent Protein Kinase Catalytic Subunits, biology, Wnt signaling pathway, Nuclear Proteins, CREB-Binding Protein, Hedgehog signaling pathway, 3. Good health, PRKACA, 030104 developmental biology, Mutation, embryonic structures, Cancer research, biology.protein, Female, Epilepsies, Partial, Hypothalamic Diseases, 030217 neurology & neurosurgery, Signal Transduction
Abstract: Hypothalamic hamartoma (HH) with gelastic epilepsy is a well-recognized drug-resistant epilepsy syndrome of early life.(1) Surgical resection allows limited access to the small deep-seated lesions that cause the disease. Here, we report the results of a search for somatic mutations in paired hamartoma- and leukocyte-derived DNA samples from 38 individuals which we conducted by using whole-exome sequencing (WES), chromosomal microarray (CMA), and targeted resequencing (TRS) of candidate genes. Somatic mutations were identified in genes involving regulation of the sonic hedgehog (Shh) pathway in 14/38 individuals (37%). Three individuals had somatic mutations in PRKACA, which encodes a cAMP-dependent protein kinase that acts as a repressor protein in the Shh pathway, and four subjects had somatic mutations in GLI3, an Shh pathway gene associated with HH. In seven other individuals, we identified two recurrent and three single brain-tissue-specific, large copy-number or loss-of-heterozygosity (LOH) variants involving multiple Shh genes, as well as other genes without an obvious biological link to the Shh pathway. The Shh pathway genes in these large somatic lesions include the ligand itself (SHH and IHH), the receptor SMO, and several other Shh downstream pathway members, including CREBBP and GLI2. Taken together, our data implicate perturbation of the Shh pathway in at least 37% of individuals with the HH epilepsy syndrome, consistent with the concept of a developmental pathway brain disease.
Published: 2016

42. Germline De Novo Mutations in GNB1 Cause Severe Neurodevelopmental Disability, Hypotonia, and Seizures

Author: Louise Bier, Fan Xia, Zhong Ren, Susan Schelley, Geoffrey Wallace, Amy L Schneider, Thomas Besnard, Tracy Dudding-Byth, David Goldstein, Benjamin Cogné, Gregory M. Enns, Xiaolin Zhu, Jill A. Rosenfeld, Edwin Guzman, Xenia Latypova, Joanne M. Nguyen, Anya Revah Politi, James J. Riviello, Sophie Colombo, Erin L. Heinzen, Candace T. Myers, Bertrand Isidor, Joline C. Dalton, Theresa A. Grebe, Michele G. Mehaffey, Peter I. Karachunski, Kwame Anyane-Yeboa, Jonathan A. Bernstein, Slavé Petrovski, Klaas J. Wierenga, Alice Basinger, Heather C Mefford, Martin G. Bialer, Pierre Corre, Ingrid E. Scheffer, Emily Becraft, Stéphane Bézieau, Natasha Shur, Sandra Mercier, Aaron Rosen, Christine Moore, Sébastien Schmitt, Sébastien Küry, Alexandrea Wadley, Parisa Hemati, and Ian Andrews
Subjects: Adult, Male, 0301 basic medicine, Adolescent, Protein Conformation, Developmental Disabilities, Biology, Bioinformatics, medicine.disease_cause, Germline, Young Adult, 03 medical and health sciences, 0302 clinical medicine, Neurodevelopmental disorder, Germline mutation, Seizures, Intellectual Disability, Report, Genetics, medicine, Humans, Missense mutation, Exome, Genetics(clinical), Child, Germ-Line Mutation, Genetics (clinical), Mutation, GTP-Binding Protein beta Subunits, Infant, medicine.disease, Hypotonia, Phenotype, 030104 developmental biology, Child, Preschool, Muscle Hypotonia, Female, medicine.symptom, GNB1, 030217 neurology & neurosurgery, Signal Transduction
Abstract: Whole-exome sequencing of 13 individuals with developmental delay commonly accompanied by abnormal muscle tone and seizures identified de novo missense mutations enriched within a sub-region of GNB1, a gene encoding the guanine nucleotide-binding protein subunit beta-1, Gβ. These 13 individuals were identified among a base of 5,855 individuals recruited for various undiagnosed genetic disorders. The probability of observing 13 or more de novo mutations by chance among 5,855 individuals is very low (p = 7.1 × 10(-21)), implicating GNB1 as a genome-wide-significant disease-associated gene. The majority of these 13 mutations affect known Gβ binding sites, which suggests that a likely disease mechanism is through the disruption of the protein interface required for Gα-Gβγ interaction (resulting in a constitutively active Gβγ) or through the disruption of residues relevant for interaction between Gβγ and certain downstream effectors (resulting in reduced interaction with the effectors). Strikingly, 8 of the 13 individuals recruited here for a neurodevelopmental disorder have a germline de novo GNB1 mutation that overlaps a set of five recurrent somatic tumor mutations for which recent functional studies demonstrated a gain-of-function effect due to constitutive activation of G protein downstream signaling cascades for some of the affected residues.
Published: 2016

43. A roadmap for precision medicine in the epilepsies

Author: Norman Delanty, Erin L. Heinzen, Ingrid E. Scheffer, Stephen F. Traynelis, Daniel H. Lowenstein, Ingo Helbig, Jack M. Parent, Wayne N. Frankel, David Goldstein, Annapurna Poduri, Dennis J. Dlugos, Steven Petrou, Heather C Mefford, Samuel F. Berkovic, and Tracy Dixon-Salazar
Subjects: Epilepsy, Research groups, business.industry, Drug discovery, Computer science, Precision medicine, medicine.disease, Data science, Article, Clinical Practice, Knowledge base, Software deployment, Drug Discovery, Mutation, medicine, Humans, Anticonvulsants, Neurology (clinical), Precision Medicine, Generalized epilepsy, business, Personal genomics
Abstract: Technological advances have paved the way for accelerated genomic discovery and are bringing precision medicine clearly into view. Epilepsy research in particular is well suited to serve as a model for the development and deployment of targeted therapeutics in precision medicine because of the rapidly expanding genetic knowledge base in epilepsy, the availability of good in-vitro and in-vivo model systems to efficiently study the biological consequences of genetic mutations, the ability to turn these models into effective drug-screening platforms, and the establishment of collaborative research groups. Moving forward, it is crucial that these collaborations are strengthened, particularly through integrated research platforms, to provide robust analyses both for accurate personal genome analysis and gene and drug discovery. Similarly, the implementation of clinical trial networks will allow the expansion of patient sample populations with genetically defined epilepsy so that drug discovery can be translated into clinical practice.
Published: 2015

44. De-novo mutations in patients with chronic ultra-refractory epilepsy with onset after age five years

Author: Ronan N. McGinty, Mark McCormack, Norman Delanty, Xiaolin Zhu, Erin L. Heinzen, Gianpiero L. Cavalleri, Daniel J. Costello, and Lisa Slattery
Subjects: 0301 basic medicine, Dynamins, Male, Pediatrics, medicine.medical_specialty, Adolescent, Genomics, 030105 genetics & heredity, 03 medical and health sciences, Epilepsy, Intellectual Disability, Intellectual disability, Exome Sequencing, Genetics, medicine, Humans, In patient, Exome, Genetic Predisposition to Disease, Age of Onset, Child, Genetics (clinical), Exome sequencing, Genetic testing, medicine.diagnostic_test, business.industry, General Medicine, Precision medicine, medicine.disease, 3. Good health, 030104 developmental biology, Mutation, Medical genetics, Anticonvulsants, Female, business
Abstract: We set out to investigate whether a de-novo paradigm could explain genetic causes of chronic ultra-refractory epilepsy, with onset later than the typical age for the epileptic encephalopathies. We performed exome sequencing on nine adult patients with MRI-negative epilepsy and no preceding intellectual disability. All had an onset of seizures after five years old and had chronic ultra-refractory epilepsy defined here as having failed more than six anti-epileptic drugs and currently experiencing ≥4 disabling seizures per month. Parents were sequenced to identify de-novo mutations and these were assessed for likelihood of pathogenicity based on the American College of Medical Genetics and Genomics (ACMG) criteria. We confirmed the presence of functional and predicted-damaging de-novo mutations in 3/9 patients. One of these pathogenic de-novo mutations, in DNM1L, was previously reported in a patient with severe epilepsy and chronic pharmacoresistance adding to the evidence for DNM1L as an epilepsy gene. Exome sequencing is a successful strategy for identifying de-novo mutations in paediatric epileptic encephalopathies and rare neurological disorders. Our study demonstrates the potential benefit of considering ultra-refractory epilepsy patients with later onset for genetic testing. Identifying genetic mutations underpinning severe epilepsy of unknown aetiology may provide new insight into the underlying biology and offers the potential for therapeutic intervention in the form of precision medicine in older patients.
Published: 2018

45. Genetics

Author: Elizabeth K. Ruzzo, Rodney A. Radtke, David B. Goldstein, and Erin L. Heinzen
Published: 2018

46. Somatic SLC35A2 variants in the brain are associated with intractable neocortical epilepsy

Author: Manu Hegde, Catherine A. Schevon, Alison M. Pack, Annapurna Poduri, Gerald A. Grant, Mohamad A. Mikati, Edward Yang, Werner Doyle, Patricia Dugan, Katherine M. Keever, Danielle McBrian, Peter B. Crino, Hart G.W. Lidov, David Zagzag, Senthilmurugan Ramalingam, Dinesh Rathakrishnan, Jurriaan M. Peters, Erin L. Heinzen, Sameer A. Sheth, Peter Canoll, Catherine Shain, Ann M. Bergin, Brenda E. Porter, Colin D. Malone, Andrew S. Allen, Jorge Samanamud, Joseph R. Madsen, Christopher M. LaCoursiere, Nicole G. Griffin, Guy M. McKhann, Cigdem I. Akman, Evan H. Baugh, Carrie R. Muh, and Melodie R. Winawer
Subjects: 0301 basic medicine, Nonsynonymous substitution, Male, Candidate gene, Pathology, Drug Resistant Epilepsy, Somatic cell, Neocortex, Neurodegenerative, Epilepsy, Phosphatidylinositol 3-Kinases, 0302 clinical medicine, 2.1 Biological and endogenous factors, Epilepsy surgery, Exome, Aetiology, Child, Neurons, TOR Serine-Threonine Kinases, Brain, Malformations of Cortical Development, Neurology, Neurological, Female, Biotechnology, medicine.medical_specialty, Monosaccharide Transport Proteins, Adolescent, Clinical Sciences, Biology, Article, 03 medical and health sciences, Young Adult, Germline mutation, Clinical Research, medicine, Genetics, Humans, Neurology & Neurosurgery, Prevention, Human Genome, Neurosciences, Cortical dysplasia, medicine.disease, Brain Disorders, 030104 developmental biology, Mutation, Neurology (clinical), 030217 neurology & neurosurgery
Abstract: OBJECTIVE Somatic variants are a recognized cause of epilepsy-associated focal malformations of cortical development (MCD). We hypothesized that somatic variants may underlie a wider range of focal epilepsy, including nonlesional focal epilepsy (NLFE). Through genetic analysis of brain tissue, we evaluated the role of somatic variation in focal epilepsy with and without MCD. METHODS We identified somatic variants through high-depth exome and ultra-high-depth candidate gene sequencing of DNA from epilepsy surgery specimens and leukocytes from 18 individuals with NLFE and 38 with focal MCD. RESULTS We observed somatic variants in 5 cases in SLC35A2, a gene associated with glycosylation defects and rare X-linked epileptic encephalopathies. Nonsynonymous variants in SLC35A2 were detected in resected brain, and absent from leukocytes, in 3 of 18 individuals (17%) with NLFE, 1 female and 2 males, with variant allele frequencies (VAFs) in brain-derived DNA of 2 to 14%. Pathologic evaluation revealed focal cortical dysplasia type Ia (FCD1a) in 2 of the 3 NLFE cases. In the MCD cohort, nonsynonymous variants in SCL35A2 were detected in the brains of 2 males with intractable epilepsy, developmental delay, and magnetic resonance imaging suggesting FCD, with VAFs of 19 to 53%; Evidence for FCD was not observed in either brain tissue specimen. INTERPRETATION We report somatic variants in SLC35A2 as an explanation for a substantial fraction of NLFE, a largely unexplained condition, as well as focal MCD, previously shown to result from somatic mutation but until now only in PI3K-AKT-mTOR pathway genes. Collectively, our findings suggest a larger role than previously recognized for glycosylation defects in the intractable epilepsies. Ann Neurol 2018.
Published: 2018

47. De novo and inherited private variants in MAP1B in periventricular nodular heterotopia

Author: Erin L Heinzen, Adam C O'Neill, Xiaolin Zhu, Andrew S Allen, Melanie Bahlo, Jamel Chelly, Ming Hui Chen, William B Dobyns, Saskia Freytag, Renzo Guerrini, Richard J Leventer, Annapurna Poduri, Stephen P Robertson, Christopher A Walsh, Mengqi Zhang, Epi4K Consortium, Epilepsy Phenome/Genome Project, univOAK, Archive ouverte, Columbia University Medical Center (CUMC), Columbia University [New York], University of Otago [Dunedin, Nouvelle-Zélande], Duke University Medical Center, Duke University [Durham], The Walter and Eliza Hall Institute of Medical Research (WEHI), University of Melbourne, 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), Les Hôpitaux Universitaires de Strasbourg (HUS), Boston Children's Hospital, University of Washington [Seattle], Seattle Children's Research Institute [Seattle, WA, USA], Università degli Studi di Firenze = University of Florence (UniFI), Harvard Medical School [Boston] (HMS), Broad Institute of MIT and Harvard (BROAD INSTITUTE), and Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston]
Subjects: Male, 0301 basic medicine, Nonsynonymous substitution, Cancer Research, Heredity, [SDV.GEN] Life Sciences [q-bio]/Genetics, QH426-470, 0302 clinical medicine, Periventricular Nodular Heterotopia, Loss of Function Mutation, Epilepsy Phenome/Genome Project, Medicine and Health Sciences, Exome, Genetics (clinical), Exome sequencing, Genetics, Database and informatics methods, Sequence analysis, Brain, Genomics, Magnetic Resonance Imaging, Penetrance, 3. Good health, Fragile X syndrome, Genetic Mapping, Neurology, Female, Transcriptome Analysis, Microtubule-Associated Proteins, Research Article, Heterozygote, Bioinformatics, Variant Genotypes, Biology, 03 medical and health sciences, Exome Sequencing, medicine, Humans, Genetic Predisposition to Disease, Allele, Molecular Biology, Alleles, DNA sequence analysis, Ecology, Evolution, Behavior and Systematics, [SDV.GEN]Life Sciences [q-bio]/Genetics, Epilepsy, Biology and Life Sciences, Computational Biology, Human Genetics, Genome Analysis, medicine.disease, Perisylvian polymicrogyria, Research and analysis methods, 030104 developmental biology, Genetic Loci, 030217 neurology & neurosurgery
Abstract: Periventricular nodular heterotopia (PVNH) is a malformation of cortical development commonly associated with epilepsy. We exome sequenced 202 individuals with sporadic PVNH to identify novel genetic risk loci. We first performed a trio-based analysis and identified 219 de novo variants. Although no novel genes were implicated in this initial analysis, PVNH cases were found overall to have a significant excess of nonsynonymous de novo variants in intolerant genes (p = 3.27x10-7), suggesting a role for rare new alleles in genes yet to be associated with the condition. Using a gene-level collapsing analysis comparing cases and controls, we identified a genome-wide significant signal driven by four ultra-rare loss-of-function heterozygous variants in MAP1B, including one de novo variant. In at least one instance, the MAP1B variant was inherited from a parent with previously undiagnosed PVNH. The PVNH was frontally predominant and associated with perisylvian polymicrogyria. These results implicate MAP1B in PVNH. More broadly, our findings suggest that detrimental mutations likely arising in immediately preceding generations with incomplete penetrance may also be responsible for some apparently sporadic diseases., Author summary Almost 20 years ago the first gene responsible for periventricular nodular heterotopia (PVNH), a disorder that leads to abnormal migration of neurons during fetal brain development, was discovered. Since that time additional genes have been identified, but collectively they only explain a minority of cases. In this work we sought to further elucidate the genetic basis of this disorder using exome sequencing of 202 individuals with PVNH. We found a clear role for de novo mutations in PVNH, although with this analysis alone we were unable to pinpoint which of the de novo mutations in novel genes caused the disease. One patient was found to have a de novo variant in MAP1B, a gene that encodes a protein that plays a role at several key steps of brain development. With further analysis of the exome sequence data we found an additional three cases with a very rare inherited variant in MAP1B. This pattern is not expected to occur by chance and therefore indicates that these variants are likely responsible for the PVNH in these patients. Further strengthing the association of MAP1B in PVNH, all of the patients with a MAP1B variant had a similar brain abnormality, and at least one of the parents who transmitted the variant to their child was also similarly affected. This work adds to a growing list of genes responsible for PVNH, illuminates new genes involved in brain development, and importantly informs us about the types of genetic variants involved in PVNH.
Published: 2018

48. NBEA : developmental disease gene with early generalized epilepsy phenotypes

Author: Hermine E. Veenstra-Knol, Rolph Pfundt, Nada Houcinat, Gregory M. Cooper, James J. Riviello, Frédéric Bilan, Servi J. C. Stevens, Susan M. Hiatt, Mary K. Kukolich, Anna Lehman, Brigitte Gilbert-Dussardier, Cédric Le Caignec, Christian Korff, Catharina M L Volker-Touw, Eva H. Brilstra, Louise Bier, Alexander P.A. Stegmann, Evan H. Baugh, Berten Ceulemans, David Goldstein, Magalie Barth, Heather C. Mefford, Elaine Pereira, Han G. Brunner, Lot Snijders Blok, E. Lopez-Rangel, Rob P.W. Rouhl, Anya Revah-Politi, Bertrand Isidor, Mathilde Pacault, Constance T. R. M. Stumpel, E. Martina Bebin, Dana Craiu, Aida Telegrafi, Marlies Kempers, Jolien Roovers, Erin L. Heinzen, Candace T. Meyers, D Barca, Tania Djémié, Nicholas Stong, Zsuzsanna Siegler, Maureen S. Mulhern, Johannes R. Lemke, Tristan T. Sands, Natalie Lippa, Nicolette S. den Hollander, Danielle McBrian, Ellen van Binsbergen, Sarah Weckhuysen, Mariëtte J.V. Hoffer, CAUSES Study, EuroEPINOMICS-RES-MAE Working Grp, MUMC+: DA KG Polikliniek (9), Klinische Genetica, RS: GROW - R4 - Reproductive and Perinatal Medicine, MUMC+: DA Klinische Genetica (5), Klinische Neurowetenschappen, RS: MHeNs - R1 - Cognitive Neuropsychiatry and Clinical Neuroscience, MUMC+: MA Med Staf Spec Neurologie (9), MUMC+: DA KG Lab Centraal Lab (9), Columbia University Medical Center (CUMC), Columbia University [New York], Maastricht University Medical Centre (MUMC), Maastricht University [Maastricht], Radboud University Medical Center [Nijmegen], Donders Institute for Brain, Cognition and Behaviour, Radboud university [Nijmegen], GeneDx [Gaithersburg, MD, USA], Centre de génétique - Centre de référence des maladies rares, anomalies du développement et syndromes malformatifs (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Equipe GAD (LNC - U1231), Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Université Bourgogne Franche-Comté [COMUE] (UBFC), Service de génétique [Angers], Université d'Angers (UA)-Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM)-PRES Université Nantes Angers Le Mans (UNAM), Department of Human Genetics, Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Centre National de la Recherche Scientifique (CNRS), Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerpen, Belgium, University of Antwerp (UA), University of Medicine and Pharmacy 'Carol Davila' Bucharest (UMPCD), Dpt de l'Enfant et de l'Adolescent, Neuropédiatrie [Genève], Hôpitaux Universitaires de Genève (HUG), University Medical Center [Utrecht], Department of Medical Genetics, Department of Medicine, Karolinska Institutet [Stockholm], Service de génétique médicale - Unité de génétique clinique [Nantes], Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes), and Centre hospitalier universitaire de Nantes (CHU Nantes)
Subjects: Male, 0301 basic medicine, Carrier Proteins/genetics, Candidate gene, Disease, Neurodevelopmental Disorders/genetics, Epilepsy, 0302 clinical medicine, Nerve Tissue Proteins/genetics, Child, Atonic seizure, Genetics, ddc:618, Phenotype, Neurology, Child, Preschool, Epilepsy, Generalized, Female, NEUROBEACHIN, Rare cancers Radboud Institute for Health Sciences [Radboudumc 9], Adolescent, Genotype, Generalized/genetics, Nerve Tissue Proteins, Biology, PATIENT, Article, 03 medical and health sciences, All institutes and research themes of the Radboud University Medical Center, medicine, Journal Article, Humans, Generalized epilepsy, AUTISM, Preschool, Gene, SPECTRUM, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], DELETION, NBEA encodes neurobeachin, medicine.disease, FRAMEWORK, 030104 developmental biology, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Neurodevelopmental Disorders, DE-NOVO MUTATIONS, Mutation, Autism, Neurology (clinical), Human medicine, Carrier Proteins, 030217 neurology & neurosurgery
Abstract: NBEA is a candidate gene for autism, and de novo variants have been reported in neurodevelopmental disease (NDD) cohorts. However, NBEA has not been rigorously evaluated as a disease gene, and associated phenotypes have not been delineated. We identified 24 de novo NBEA variants in patients with NDD, establishing NBEA as an NDD gene. Most patients had epilepsy with onset in the first few years of life, often characterized by generalized seizure types, including myoclonic and atonic seizures. Our data show a broader phenotypic spectrum than previously described, including a myoclonic-astatic epilepsy-like phenotype in a subset of patients. Ann Neurol 2018;84:796-803
Published: 2018

49. A case-control collapsing analysis identifies epilepsy genes implicated in trio sequencing studies focused on de novo mutations

Author: Davide Mei, Andrew S. Allen, Zhong Ren, Renzo Guerrini, Joshua Bridgers, Ailbhe O’Driscoll-Collins, Annapurna Poduri, Ingrid E. Scheffer, David Goldstein, Samuel F. Berkovic, Raghavendra Padmanabhan, Brett Copeland, Xiaolin Zhu, Daniel H. Lowenstein, Sitharthan Kamalakaran, Erin L. Heinzen, and Cooper, Gregory M
Subjects: 0301 basic medicine, Male, Cancer Research, Potassium Channels, DNA Mutational Analysis, Gene Sequencing, Genome-wide association study, Potassium Channels, Sodium-Activated, Neurodegenerative, Genome, Whole Exome Sequencing, Sequencing techniques, Mathematical and Statistical Techniques, Medicine and Health Sciences, 2.1 Biological and endogenous factors, DNA sequencing, Genome Sequencing, Aetiology, Genetics (clinical), Exome sequencing, Genes, Dominant, Genetics, Principal Component Analysis, NAV1.2 Voltage-Gated Sodium Channel, Genomics, Neurology, Physical Sciences, Female, Sodium-Activated, Statistics (Mathematics), Research Article, Biotechnology, lcsh:QH426-470, Permutation, Epilepsy--Genetic aspects, Nerve Tissue Proteins, Biology, 03 medical and health sciences, Munc18 Proteins, Genomic Medicine, Exome Sequencing, Humans, Dominant, Statistical Methods, Allele, Molecular Biology, Gene, Alleles, Ecology, Evolution, Behavior and Systematics, Trio exome sequencing, Epilepsy, Biology and life sciences, Discrete Mathematics, Human Genome, Computational Biology, Mutation (Biology), Genome Analysis, Research and analysis methods, lcsh:Genetics, Molecular biology techniques, 030104 developmental biology, Genes, Combinatorics, Genetic Loci, FOS: Biological sciences, Case-Control Studies, Multivariate Analysis, Mutation, Human genome, Nucleotide sequence, Mathematics, Genome-Wide Association Study, Developmental Biology
Abstract: Trio exome sequencing has been successful in identifying genes with de novo mutations (DNMs) causing epileptic encephalopathy (EE) and other neurodevelopmental disorders. Here, we evaluate how well a case-control collapsing analysis recovers genes causing dominant forms of EE originally implicated by DNM analysis. We performed a genome-wide search for an enrichment of "qualifying variants" in protein-coding genes in 488 unrelated cases compared to 12,151 unrelated controls. These "qualifying variants" were selected to be extremely rare variants predicted to functionally impact the protein to enrich for likely pathogenic variants. Despite modest sample size, three known EE genes (KCNT1, SCN2A, and STXBP1) achieved genome-wide significance (p, Author summary Trio exome sequencing and de novo mutation (DNM) analysis has been the main approach to discovering genes responsible for severe sporadic disorders, including a range of neurodevelopmental disorders. This approach requires sequencing parents, identifying DNMs from trio sequence data, and comparing the observed rate of DNMs to the expected. In this study, we adopted a case-control design, performed a gene-based collapsing analysis, and rediscovered several of the epileptic encephalopathy (EE) genes originally implicated by DNM analysis of EE trios. Our collapsing analysis focused on ultra-rare, highly impactful variants (“qualifying variants”) by filtering against large-scale population datasets, and this approach revealed that most of the standing variation can be filtered out and DNMs are enriched in “qualifying variants”. Our study suggests that a case-control analysis approach can be used to identify disease genes with causal mutations that are predominantly de novo in place of trio-based analysis methods. This offers an efficient and cost effective alternative approach when large-scale trio sequencing is not possible.
Published: 2017

50. A functional correlate of severity in alternating hemiplegia of childhood

Author: Dana Jazayeri, Melody Li, David Goldstein, Erin L. Heinzen, Ben Corry, K. Melodi McSweeney, and Steven Petrou
Subjects: Male, Models, Molecular, Na+/K+ ATPase, Cation binding, Patch-Clamp Techniques, Microinjections, ATPase, Hemiplegia, Membrane Potentials, lcsh:RC321-571, Xenopus laevis, Transduction, Genetic, ATP1A3, Proton transport, medicine, Animals, Humans, Na+/K+-ATPase, lcsh:Neurosciences. Biological psychiatry. Neuropsychiatry, Genetics, biology, Alternating hemiplegia of childhood, Wild type, medicine.disease, Molecular biology, Transport protein, Protein Transport, Neurology, Child, Preschool, Mutation, Oocytes, biology.protein, Female, Sodium-Potassium-Exchanging ATPase
Abstract: Objective Mutations in ATP1A3, the gene that encodes the α3 subunit of the Na+/K+ ATPase, are the primary cause of alternating hemiplegia of childhood (AHC). Correlations between different mutations and AHC severity were recently reported, with E815K identified in severe and D801N and G947R in milder cases. This study aims to explore the molecular pathological mechanisms in AHC and to identify functional correlates for mutations associated with different levels of disease severity. Methods Human wild type ATP1A3, and E815K, D801N and G947R mutants were expressed in Xenopus laevis oocytes and Na+/K+ ATPase function measured. Structural homology models of the human α3 subunit containing AHC mutations were created. Results The AHC mutations examined all showed similar levels of reduction in forward cycling. Wild type forward cycling was reduced by coexpression with any mutant, indicating dominant negative interactions. Proton transport was measured and found to be selectively impaired only in E815K. Homology modeling showed that D801 and G947 lie within or near known cation binding sites while E815 is more distal. Despite its effect on proton transport, E815K was also distant from the proposed proton transport route. Interpretation Loss of forward cycling and dominant negativity are common and likely necessary pathomechanisms for AHC. In addition, loss of proton transport correlated with severity of AHC. D801N and G947R are likely to directly disrupt normal Na+/K+ binding while E815K may disrupt forward cycling and proton transport via allosteric mechanisms yet to be elucidated.
Published: 2015

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