Author: "Erin L. Heinzen" / Topic: humans - Searchworks@Jio Institute Digital Library Search Results

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1. 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

2. 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

3. 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

4. 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

5. 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

6. 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: Multifactorial Inheritance, Epilepsy, Humans, Epilepsy, Generalized, Genetic Predisposition to Disease, General Medicine, Epileptic Syndromes, General Biochemistry, Genetics and Molecular Biology, Genome-Wide Association Study
Abstract: 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.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.Patients with familial epilepsies had higher epilepsy PRS compared to population controls (OR 1·20, pThe 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.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

7. 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

8. 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

9. 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

10. 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

11. 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

12. 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

13. 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

14. 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

15. 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

16. 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

17. 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

18. 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

19. 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

20. 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

21. 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

22. 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

23. 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

24. 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

25. 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

26. 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

27. 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

28. 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

29. 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

30. 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

31. Further delineation of the clinical spectrum of de novo TRIM8 truncating mutations

Author: Véronique Darmency, Sharon Whiting, Laurence Faivre, Jean-François Deleuze, Daniel H. Lowenstein, Julien Thevenon, Rebecca Hernan, Matthew A. Lines, Orly Elpeleg, Yannis Duffourd, Corinne Antignac, Mirna Assoum, Erin L. Heinzen, Martine Lemesle, Christel Thauvin-Robinet, Aurélie Bertholet-Thomas, Wendy K. Chung, Orrin Devinsky, Eric B. Geller, Vincent des Portes, Alexandre Belot, Simon Edvardson, 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, Children's Hospital of Eastern Ontario, Department of Genetics and Metabolic Diseases and the Monique and Jacques Roboh Department of Genetic Research, Hadassah Hebrew University Medical Center [Jerusalem], Service de Neurophysiologie Clinique (CHU Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), New York University School of Medicine (NYU), New York University School of Medicine, NYU System (NYU)-NYU System (NYU), Columbia University Medical Center (CUMC), Columbia University [New York], Imagine - Institut des maladies génétiques (IMAGINE - U1163), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Necker Enfants-Malades (INEM - UM 111 (UMR 8253 / U1151)), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), CHU Necker - Enfants Malades [AP-HP], Centre National de Génotypage (CNG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut des Sciences cognitives Marc Jeannerod - Laboratoire sur le langage, le cerveau et la cognition (L2C2), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Réponse immunitaire innée dans les maladies infectieuses et auto-immunes – Innate immunity in infectious and autoimmune diseases, Centre International de Recherche en Infectiologie - UMR (CIRI), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Service de néphrologie, rhumatologie et dermatologie pédiatriques [Hôpital Femme Mère Enfant, HCL], Hospices Civils de Lyon (HCL)-Hôpital Mère Enfant, FHU TRANSLAD, Centre de génétique - Centre de référence des maladies rares, anomalies du développement et syndromes malformatifs (CHU de Dijon), University of California [San Francisco] (UCSF), University of California, Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Centre International de Recherche en Infectiologie (CIRI), 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)-École normale supérieure de Lyon (ENS de Lyon)-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), FHU TRANSLAD (CHU de Dijon), University of California [San Francisco] (UC San Francisco), University of California (UC), 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), École normale supérieure - Lyon (ENS Lyon)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL)
Subjects: 0301 basic medicine, Male, Adolescent, Nerve Tissue Proteins, Bioinformatics, whole exome sequencing, 03 medical and health sciences, Epilepsy, Tripartite Motif, Genetics, medicine, Humans, TRIM8, Amino Acid Sequence, Child, Gene, Genetics (clinical), De novo mutations, Exome sequencing, business.industry, nephrotic syndrome, Epileptic encephalopathy, Infant, Newborn, Infant, medicine.disease, Phenotype, 3. Good health, 030104 developmental biology, epileptic encephalopathy, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Child, Preschool, Mutation, Female, business, Carrier Proteins, Nephrotic syndrome
Abstract: IF 2.264; International audience; De novo mutations of the TRIM8 gene, which codes for a tripartite motif protein, have been identified using whole exome sequencing (WES) in two patients with epileptic encephalopathy (EE), but these reports were not sufficient to conclude that TRIM8 was a novel gene responsible for EE. Here we report four additional patients presenting with EE and de novo truncating mutations of TRIM8 detected by WES, and give further details of the patient previously reported by the Epi4K consortium. Epilepsy of variable severity was diagnosed in children aged 2 months to 3.5 years of age. All patients had developmental delay of variable severity with no or very limited language, often associated with behavioral anomalies and unspecific facial features or MRI brain abnormalities. The phenotypic variability observed in these patients appeared related to the severity of the epilepsy. One patient presented pharmacoresistant EE with regression, recurrent infections and nephrotic syndrome, compatible with the brain and kidney expression of TRIM8. Interestingly, all mutations were located at the highly conserved C-terminus section of TRIM8. This collaborative study confirms that TRIM8 is a novel gene responsible for EE, possibly associated with nephrotic syndrome. This report brings new evidence on the pathogenicity of TRIM8 mutations and highlights the value of data-sharing to delineate the phenotypic characteristics and biological basis of extremely rare disorders.
Published: 2017

32. Common genetic variation and susceptibility to partial epilepsies: a genome-wide association study

Author: Paul M. Matthews, Anne-Mari Kantanen, Dena G. Hernandez, David A. Hosford, Mohamad A. Mikati, Heinz Gregor Wieser, Sarah K. Tate, Günter Krämer, Reetta Kälviäinen, Jörg Hansen, Lefkos T. Middleton, Bernhard J. Steinhoff, Dominik Zumsteg, Josemir W. Sander, Massimo Pandolfo, Leslie Amos, Norman Delanty, Saud Alhusaini, David Goldstein, Marvin Johnson, Krishna Chinthapalli, John S. Duncan, Marcos Ortega, Sanjay M. Sisodiya, Leif Gjerstad, Aatif M. Husain, Chantal Depondt, Kai Eriksson, Dalia Kasperavičiūtė, David Leppert, Jenny Jamnadas-Khoda, Erin L. Heinzen, Terhi Peuralinna, Claudia B. Catarino, Rodney A. Radtke, Colin P. Doherty, Kevin V. Shianna, Lisa M. S. Clayton, Luis O. Caboclo, Thomas Dorn, William Gallentine, Nicholas W. Wood, Kjell Heuser, Gianpiero L. Cavalleri, Rachel A. Gibson, and University of Zurich
Subjects: Male, Internationality, LOCI, Genome-wide association study, ENVIRONMENTAL-FACTORS, 16P13.11 PREDISPOSE, 0302 clinical medicine, common variants, genetics, POPULATION, Genetics, 0303 health sciences, education.field_of_study, 11 Medical And Health Sciences, Syndrome, ETIOLOGY, 3. Good health, 2728 Neurology (clinical), DISEASES, Female, Life Sciences & Biomedicine, partial epilepsy, Population, Clinical Neurology, TWIN, Single-nucleotide polymorphism, 610 Medicine & health, Biology, Polymorphism, Single Nucleotide, 17 Psychology And Cognitive Sciences, 03 medical and health sciences, Genetic variation, LINKAGE, Genetic predisposition, Humans, Genetic Predisposition to Disease, education, METAANALYSIS, 030304 developmental biology, Science & Technology, Neurology & Neurosurgery, Genetic heterogeneity, Neurosciences, Genetic Variation, Original Articles, Heritability, Genetic architecture, 10040 Clinic for Neurology, genome-wide association, SEIZURES, Neurosciences & Neurology, Epilepsies, Partial, Neurology (clinical), 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract: Partial epilepsies have a substantial heritability. However, the actual genetic causes are largely unknown. In contrast to many other common diseases for which genetic association-studies have successfully revealed common variants associated with disease risk, the role of common variation in partial epilepsies has not yet been explored in a well-powered study. We undertook a genome-wide association-study to identify common variants which influence risk for epilepsy shared amongst partial epilepsy syndromes, in 3445 patients and 6935 controls of European ancestry. We did not identify any genome-wide significant association. A few single nucleotide polymorphisms may warrant further investigation. We exclude common genetic variants with effect sizes above a modest 1.3 odds ratio for a single variant as contributors to genetic susceptibility shared across the partial epilepsies. We show that, at best, common genetic variation can only have a modest role in predisposition to the partial epilepsies when considered across syndromes in Europeans. The genetic architecture of the partial epilepsies is likely to be very complex, reflecting genotypic and phenotypic heterogeneity. Larger meta-analyses are required to identify variants of smaller effect sizes (odds ratio
Published: 2017

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

Author: Andrew S Allen, Susannah T Bellows, Samuel F Berkovic, Joshua Bridgers, Rosemary Burgess, Gianpiero Cavalleri, Seo-Kyung Chung, Patrick Cossette, Norman Delanty, Dennis Dlugos, Michael P Epstein, Catharine Freyer, David B Goldstein, Erin L Heinzen, Michael S Hildebrand, Michael R Johnson, Ruben Kuzniecky, Daniel H Lowenstein, Anthony G Marson, Richard Mayeux, Caroline Mebane, Heather C Mefford, Terence J O'Brien, Ruth Ottman, Steven Petrou, Slavgé Petrovski, William O Pickrell, Annapurna Poduri, Rodney A Radtke, Mark I Rees, Brigid M Regan, Zhong Ren, Ingrid E Scheffer, Graeme J Sills, Rhys H Thomas, Quanli Wang, Bassel Abou-Khalil, Brian K Alldredge, Dina Amrom, Eva Andermann, Frederick Andermann, Jocelyn F. Bautista, Judith Bluvstein, Alex Boro, Gregory D Cascino, Damian Consalvo, Patricia Crumrine, Orrin Devinsky, Miguel Fiol, Nathan B Fountain, Jacqueline French, Daniel Friedman, Eric B Geller, Tracy Glauser, Simon Glynn, Kevin Haas, Sheryl R Haut, Jean Hayward, Sandra L Helmers, Sucheta Joshi, Andres Kanner, Heidi E Kirsch, Robert C Knowlton, Eric H Kossoff, Rachel Kuperman, Paul V Motika, Edward J Novotny, Juliann M Paolicchi, Jack M Parent, Kristen Park, Lynette G Sadleir, Renée A. Shellhaas, Elliott H Sherr, Jerry J. Shih, Shlomo Shinnar, Rani K Singh, Joseph Sirven, Michael C Smith, Joseph Sullivan, Liu Lin Thio, Anu Venkat, Eileen P.G Vining, Gretchen K Von Allmen, Judith L Weisenberg, Peter Widdess-Walsh, Melodie R Winawer, and Imperial College Healthcare NHS Trust- BRC Funding
Subjects: 0301 basic medicine, medicine.medical_specialty, Population, Disease, Bioinformatics, 03 medical and health sciences, Epilepsy, 0302 clinical medicine, Epilepsy Phenome/Genome Project, Genetic variation, medicine, Humans, Exome, Genetic Predisposition to Disease, education, Psychiatry, education.field_of_study, Neurology & Neurosurgery, business.industry, Genetic Variation, 1103 Clinical Sciences, Sequence Analysis, DNA, medicine.disease, Comorbidity, R1, 030104 developmental biology, Case-Control Studies, Epilepsy syndromes, Epilepsy, Generalized, Epilepsies, Partial, Neurology (clinical), 1109 Neurosciences, business, 030217 neurology & neurosurgery
Abstract: Summary Background Despite progress in understanding the genetics of rare epilepsies, the more common epilepsies have proven less amenable to traditional gene-discovery analyses. We aimed to assess the contribution of ultra-rare genetic variation to common epilepsies. Methods We did a case-control sequencing study with exome sequence data from unrelated individuals clinically evaluated for one of the two most common epilepsy syndromes: familial genetic generalised epilepsy, or familial or sporadic non-acquired focal epilepsy. Individuals of any age were recruited between Nov 26, 2007, and Aug 2, 2013, through the multicentre Epilepsy Phenome/Genome Project and Epi4K collaborations, and samples were sequenced at the Institute for Genomic Medicine (New York, USA) between Feb 6, 2013, and Aug 18, 2015. To identify epilepsy risk signals, we tested all protein-coding genes for an excess of ultra-rare genetic variation among the cases, compared with control samples with no known epilepsy or epilepsy comorbidity sequenced through unrelated studies. Findings We separately compared the sequence data from 640 individuals with familial genetic generalised epilepsy and 525 individuals with familial non-acquired focal epilepsy to the same group of 3877 controls, and found significantly higher rates of ultra-rare deleterious variation in genes established as causative for dominant epilepsy disorders (familial genetic generalised epilepsy: odd ratio [OR] 2·3, 95% CI 1·7–3·2, p=9·1 × 10 −8 ; familial non-acquired focal epilepsy 3·6, 2·7–4·9, p=1·1 × 10 −17 ). Comparison of an additional cohort of 662 individuals with sporadic non-acquired focal epilepsy to controls did not identify study-wide significant signals. For the individuals with familial non-acquired focal epilepsy, we found that five known epilepsy genes ranked as the top five genes enriched for ultra-rare deleterious variation. After accounting for the control carrier rate, we estimate that these five genes contribute to the risk of epilepsy in approximately 8% of individuals with familial non-acquired focal epilepsy. Our analyses showed that no individual gene was significantly associated with familial genetic generalised epilepsy; however, known epilepsy genes had lower p values relative to the rest of the protein-coding genes (p=5·8 × 10 −8 ) that were lower than expected from a random sampling of genes. Interpretation We identified excess ultra-rare variation in known epilepsy genes, which establishes a clear connection between the genetics of common and rare, severe epilepsies, and shows that the variants responsible for epilepsy risk are exceptionally rare in the general population. Our results suggest that the emerging paradigm of targeting of treatments to the genetic cause in rare devastating epilepsies might also extend to a proportion of common epilepsies. These findings might allow clinicians to broadly explain the cause of these syndromes to patients, and lay the foundation for possible precision treatments in the future. Funding National Institute of Neurological Disorders and Stroke (NINDS), and Epilepsy Research UK.
Published: 2017

34. De Novo Mutations in Synaptic Transmission Genes Including DNM1 Cause Epileptic Encephalopathies

Author: Silke Appenzeller, Rudi Balling, Nina Barisic, Stéphanie Baulac, Hande Caglayan, Dana Craiu, Peter De Jonghe, Christel Depienne, Petia Dimova, Tania Djémié, Padhraig Gormley, Renzo Guerrini, Ingo Helbig, Helle Hjalgrim, Dorota Hoffman-Zacharska, Johanna Jähn, Karl Martin Klein, Bobby Koeleman, Vladimir Komarek, Roland Krause, Gregor Kuhlenbäumer, Eric Leguern, Anna-Elina Lehesjoki, Johannes R. Lemke, Holger Lerche, Tarja Linnankivi, Carla Marini, Patrick May, Rikke S. Møller, Hiltrud Muhle, Deb Pal, Aarno Palotie, Manuela Pendziwiat, Angela Robbiano, Filip Roelens, Felix Rosenow, Kaja Selmer, Jose M. Serratosa, Sanjay Sisodiya, Ulrich Stephani, Katalin Sterbova, Pasquale Striano, Arvid Suls, Tiina Talvik, Sarah von Spiczak, Yvonne Weber, Sarah Weckhuysen, Federico Zara, Bassel Abou-Khalil, Brian K. Alldredge, Eva Andermann, Frederick Andermann, Dina Amrom, Jocelyn F. Bautista, Samuel F. Berkovic, Judith Bluvstein, Alex Boro, Gregory Cascino, Damian Consalvo, Patricia Crumrine, Orrin Devinsky, Dennis Dlugos, Michael P. Epstein, Miguel Fiol, Nathan B. Fountain, Jacqueline French, Daniel Friedman, Eric B. Geller, Tracy Glauser, Simon Glynn, Kevin Haas, Sheryl R. Haut, Jean Hayward, Sandra L. Helmers, Sucheta Joshi, Andres Kanner, Heidi E. Kirsch, Robert C. Knowlton, Eric H. Kossoff, Rachel Kuperman, Ruben Kuzniecky, Daniel H. Lowenstein, Shannon M. McGuire, Paul V. Motika, Edward J. Novotny, Ruth Ottman, Juliann M. Paolicchi, Jack Parent, Kristen Park, Annapurna Poduri, Lynette Sadleir, Ingrid E. Scheffer, Renée A. Shellhaas, Elliott Sherr, Jerry J. Shih, Rani Singh, Joseph Sirven, Michael C. Smith, Joe Sullivan, Liu Lin Thio, Anu Venkat, Eileen P.G. Vining, Gretchen K. Von Allmen, Judith L. Weisenberg, Peter Widdess-Walsh, Melodie R. Winawer, Andrew S. Allen, Patrick Cossette, Norman Delanty, Evan E. Eichler, David B. Goldstein, Yujun Han, Erin L. Heinzen, Michael R. Johnson, Anthony G. Marson, Heather C. Mefford, Sahar Esmaeeli Nieh, Terence J. O’Brien, Stephen Petrou, Slavé Petrovski, Elizabeth K. Ruzzo, Neuroscience Center, Research Programs Unit, Department of Medical and Clinical Genetics, Research Programme for Molecular Neurology, Institute for Molecular Medicine Finland, Genomics of Neurological and Neuropsychiatric Disorders, EuroEPINOMICS-RES Consortium, Epilepsy Phenome Genome Project, and Epi4K Consortium
Subjects: 0301 basic medicine, Male, Proband, INTELLECTUAL DISABILITY, Type I, Bioinformatics, medicine.disease_cause, Infantile, Synaptic Transmission, Spasms, Cohort Studies, Epilepsy, 0302 clinical medicine, Receptors, SCHIZOPHRENIA, STXBP1, Exome, Gene Regulatory Networks, Protein Interaction Maps, Dynamin I, Genetics (clinical), Genetics, 0303 health sciences, Mutation, education.field_of_study, Medicine (all), Genome project, Fatty Acid Synthase, Type I, Fatty Acid Synthase, Female, APHASIA, Spasms, Infantile, DYNAMIN-1, EPILEPSIES, ENDOCYTOSIS, Population, SPECTRUM DISORDERS, Phenome, Neurotransmission, Biology, GNAO1, Article, 03 medical and health sciences, GRIN2A MUTATIONS, medicine, Humans, AUTISM, Infant, Newborn, Lennox Gastaut Syndrome, Receptors, GABA-B, Ryanodine Receptor Calcium Release Channel, education, Gene, De novo mutations, 030304 developmental biology, GABA-B, 3112 Neurosciences, Infant, Correction, Newborn, medicine.disease, Human genetics, 030104 developmental biology, DNM1, PATTERNS, Human medicine, 030217 neurology & neurosurgery, Lennox–Gastaut syndrome
Abstract: Emerging evidence indicates that epileptic encephalopathies are genetically highly heterogeneous, underscoring the need for large cohorts of well-characterized individuals to further define the genetic landscape. Through a collaboration between two consortia (EuroEPINOMICS and Epi4K/EPGP), we analyzed exome-sequencing data of 356 trios with the "classical" epileptic encephalopathies, infantile spasms and Lennox Gastaut syndrome, including 264 trios previously analyzed by the Epi4K/EPGP consortium. In this expanded cohort, we find 429 de nova mutations, including de novo mutations in DNM1 in five individuals and de nova mutations in GABBR2, FASN, and RYR3 in two individuals each. Unlike previous studies, this cohort is sufficiently large to show a significant excess of de nova mutations in epileptic encephalopathy probands compared to the general population using a likelihood analysis (p = 8.2 x 10(-4)), supporting a prominent role for de novo mutations in epileptic encephalopathies. We bring statistical evidence that mutations in DNM1 cause epileptic encephalopathy, find suggestive evidence for a role of three additional genes, and show that at least 12% of analyzed individuals have an identifiable causal de novo mutation. Strikingly, 75% of mutations in these probands are predicted to disrupt a protein involved in regulating synaptic transmission, and there is a significant enrichment of de nova mutations in genes in this pathway in the entire cohort as well. These findings emphasize an important role for synaptic dysregulation in epileptic encephalopathies, above and beyond that caused by ion channel dysfunction.
Published: 2017

35. Phenotypic analysis of 303 multiplex families with common epilepsies

Author: Eileen P.G. Vining, Patrick Cossette, Mike Smith, P. E. M. Smith, Zaid Afawi, G. D. Cascino, Jocelyn F. Bautista, EJ Cops, Robert C. Knowlton, Tracy A. Glauser, Anu Venkat, Peter Widdess-Walsh, Sara Kivity, Mark I. Rees, Kevin McKenna, Amos D. Korczyn, Douglas E. Crompton, Saul A. Mullen, Heidi E. Kirsch, Nathan B. Fountain, Sheryl R. Haut, Slavé Petrovski, Andrew S. Allen, Sarah I. Garry, Anthony G Marson, Bassel Abou-Khalil, Rhys H. Thomas, Jerry J. Shih, Michael P. Epstein, Eric H. Kossoff, Winawer, Liu Lin Thio, Daniel H. Lowenstein, Dennis J. Dlugos, Rosemary Burgess, Eric B. Geller, Micheline Gravel, Jack M. Parent, Simon Glynn, Norman Delanty, Rebecca Loeb, Terence J. O'Brien, Ingrid E. Scheffer, Joseph I Sirven, William O. Pickrell, Judith L.Z. Weisenberg, Mark McCormack, Erin L. Heinzen, Judith Bluvstein, David Goldstein, Hadassa Goldberg-Stern, Sarah Paterson, Rinki Singh, Sabrina Cristofaro, Ruth Ottman, Susannah T. Bellows, R. Kuzniecky, Paul V. Motika, Heather C Mefford, Catharine Freyer, Annapurna Poduri, Juliann M. Paolicchi, Orrin Devinsky, Kevin Haas, Samuel F. Berkovic, Von, Allmen, G, and Lynette G. Sadleir
Subjects: 0301 basic medicine, Male, Adolescent, Idiopathic generalized epilepsy, 03 medical and health sciences, Epilepsy, Young Adult, 0302 clinical medicine, Sex Factors, medicine, Humans, Generalized epilepsy, Age of Onset, Child, Genetics, Family Health, business.industry, Family aggregation, Original Articles, medicine.disease, Pedigree, Rolandic epilepsy, 030104 developmental biology, Phenotype, Child, Preschool, Epilepsy syndromes, Epilepsy, Generalized, Female, Neurology (clinical), Juvenile myoclonic epilepsy, Age of onset, business, 030217 neurology & neurosurgery
Abstract: Gene identification in epilepsy has mainly been limited to large families segregating genes of major effect and de novo mutations in epileptic encephalopathies. Many families that present with common non-acquired focal epilepsies and genetic generalized epilepsies remain unexplained. We assembled a cohort of 'genetically enriched' common epilepsies by collecting and phenotyping families containing multiple individuals with unprovoked seizures. We aimed to determine if specific clinical epilepsy features aggregate within families, and whether this segregation of phenotypes may constitute distinct 'familial syndromes' that could inform genomic analyses. Families with three or more individuals with unprovoked seizures were studied across multiple international centres. Affected individuals were phenotyped and classified according to specific electroclinical syndromes. Families were categorized based on syndromic groupings of affected family members, examined for pedigree structure and phenotypic patterns and, where possible, assigned specific familial epilepsy syndromes. A total of 303 families were assembled and analysed, comprising 1120 affected phenotyped individuals. Of the 303 families, 117 exclusively segregated generalized epilepsy, 62 focal epilepsy, and 22 were classified as genetic epilepsy with febrile seizures plus. Over one-third (102 families) were observed to have mixed epilepsy phenotypes: 78 had both generalized and focal epilepsy features within the same individual (n = 39), or within first or second degree relatives (n = 39). Among the genetic generalized epilepsy families, absence epilepsies were found to cluster within families independently of juvenile myoclonic epilepsy, and significantly more females were affected than males. Of the 62 familial focal epilepsy families, two previously undescribed familial focal syndrome patterns were evident: 15 families had posterior quadrant epilepsies, including seven with occipito-temporal localization and seven with temporo-parietal foci, and four families displayed familial focal epilepsy of childhood with multiple affected siblings that was suggestive of recessive inheritance. The findings suggest (i) specific patterns of syndromic familial aggregation occur, including newly recognized forms of familial focal epilepsy; (ii) although syndrome-specificity usually occurs in multiplex families, the one-third of families with features of both focal and generalized epilepsy is suggestive of shared genetic determinants; and (iii) patterns of features observed across families including pedigree structure, sex, and age of onset may hold clues for future gene identification. Such detailed phenotypic information will be invaluable in the conditioning and interpretation of forthcoming sequencing data to understand the genetic architecture and inter-relationships of the common epilepsy syndromes.
Published: 2017

36. Utilizing Population Controls in Rare-Variant Case-Parent Association Tests

Author: David Goldstein, Yu Jiang, Michael P. Epstein, Erin L. Heinzen, Glen A. Satten, Andrew S. Allen, and Yujun Han
Subjects: Parents, Linkage disequilibrium, Genotype, Population, Genome-wide association study, Biology, Population stratification, Linkage Disequilibrium, Article, Rare Diseases, Gene Frequency, Genetic variation, Statistics, Genetics, Humans, Computer Simulation, Genetic Predisposition to Disease, Genetics(clinical), education, Allele frequency, Genetics (clinical), Statistic, education.field_of_study, Epilepsy, Models, Genetic, Genetic Variation, Transmission disequilibrium test, Control Groups, Genetics, Population, Phenotype, Genetic Loci, Genome-Wide Association Study
Abstract: There is great interest in detecting associations between human traits and rare genetic variation. To address the low power implicit in single-locus tests of rare genetic variants, many rare-variant association approaches attempt to accumulate information across a gene, often by taking linear combinations of single-locus contributions to a statistic. Using the right linear combination is key—an optimal test will up-weight true causal variants, down-weight neutral variants, and correctly assign the direction of effect for causal variants. Here, we propose a procedure that exploits data from population controls to estimate the linear combination to be used in an case-parent trio rare-variant association test. Specifically, we estimate the linear combination by comparing population control allele frequencies with allele frequencies in the parents of affected offspring. These estimates are then used to construct a rare-variant transmission disequilibrium test (rvTDT) in the case-parent data. Because the rvTDT is conditional on the parents’ data, using parental data in estimating the linear combination does not affect the validity or asymptotic distribution of the rvTDT. By using simulation, we show that our new population-control-based rvTDT can dramatically improve power over rvTDTs that do not use population control information across a wide variety of genetic architectures. It also remains valid under population stratification. We apply the approach to a cohort of epileptic encephalopathy (EE) trios and find that dominant (or additive) inherited rare variants are unlikely to play a substantial role within EE genes previously identified through de novo mutation studies.
Published: 2014

37. Gaps and opportunities in refractory status epilepticus research in children: A multi-center approach by the Pediatric Status Epilepticus Research Group (pSERG)

Author: James J. Riviello, David Goldstein, Erin L. Heinzen, Joshua L. Goldstein, Kevin E. Chapman, Howard P. Goodkin, Katrina Peariso, Mohamad A. Mikati, Cecil D. Hahn, Iván Sánchez Fernández, Jessica L. Carpenter, Satish Agadi, Tobias Loddenkemper, John Pestian, Robert C. Tasker, Margie Ream, William D. Gaillard, Tracy A. Glauser, Ravindra Arya, Korwyn Williams, Nicholas S. Abend, and Sookee An
Subjects: medicine.medical_specialty, Research network, Clinical Neurology, Status epilepticus, Controlled studies, Article, Clinical knowledge, Benzodiazepines, 03 medical and health sciences, 0302 clinical medicine, Refractory, Seizures, 030225 pediatrics, Treatment guidelines, medicine, Humans, Multicenter Studies as Topic, Initial treatment, Limited evidence, Child, Intensive care medicine, Children, Evidence-Based Medicine, Epilepsy, business.industry, Treatment options, General Medicine, 3. Good health, Neurology, Research Design, Anticonvulsants, Neurology (clinical), medicine.symptom, business, 030217 neurology & neurosurgery, Pediatric population
Abstract: Purpose: Status epilepticus (SE) is a life-threatening condition that can be refractory to initial treatment. Randomized controlled studies to guide treatment choices, especially beyond first-line drugs, are not available. This report summarizes the evidence that guides the management of refractory convulsive SE (RCSE) in children, defines gaps in our clinical knowledge and describes the development and works of the ‘pediatric Status Epilepticus Research Group’ (pSERG). Methods: A literature review was performed to evaluate current gaps in the pediatric SE and RCSE literature. In person and online meetings helped to develop and expand the pSERG network. Results: The care of pediatric RCSE is largely based on extrapolations of limited evidence derived from adult literature and supplemented with case reports and case series in children. No comparative effectiveness trials have been performed in the pediatric population. Gaps in knowledge include risk factors for SE, biomarkers of SE and RCSE, second-and third-line treatment options, and long-term outcome. Conclusion: The care of children with RCSE is based on limited evidence. In order to address these knowledge gaps, the multicenter pSERG was established to facilitate prospective collection, analysis, and sharing of de-identified data and biological specimens from children with RCSE. These data will allow identification of treatment strategies associated with better outcomes and delineate evidence-based interventions to improve the care of children with SE.
Published: 2014

38. Reply

Author: Chantal, Depondt, Erin L, Heinzen, and David B, Goldstein
Subjects: Mutation, Humans, Protein-Tyrosine Kinases, Spasms, Infantile
Published: 2016

39. Annotating pathogenic non-coding variants in genic regions

Author: Quanli Wang, Zhong Ren, Erin L. Heinzen, Kelly Schoch, K. Melodi McSweeney, Sahar Gelfman, David Goldstein, Michael J. Boland, Slavé Petrovski, Francesca La Carpia, Fanni Ratzon, and Matt Halvorsen
Subjects: 0301 basic medicine, Science, General Physics and Astronomy, Biology, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, 0302 clinical medicine, Gene Frequency, Genetic variation, Databases, Genetic, Humans, Exome, Allele frequency, Gene, Exome sequencing, Genetics, Multidisciplinary, Epilepsy, Intron, Genetic Variation, Molecular Sequence Annotation, General Chemistry, Introns, Minor allele frequency, 030104 developmental biology, Human genome, 030217 neurology & neurosurgery
Abstract: Identifying the underlying causes of disease requires accurate interpretation of genetic variants. Current methods ineffectively capture pathogenic non-coding variants in genic regions, resulting in overlooking synonymous and intronic variants when searching for disease risk. Here we present the Transcript-inferred Pathogenicity (TraP) score, which uses sequence context alterations to reliably identify non-coding variation that causes disease. High TraP scores single out extremely rare variants with lower minor allele frequencies than missense variants. TraP accurately distinguishes known pathogenic and benign variants in synonymous (AUC = 0.88) and intronic (AUC = 0.83) public datasets, dismissing benign variants with exceptionally high specificity. TraP analysis of 843 exomes from epilepsy family trios identifies synonymous variants in known epilepsy genes, thus pinpointing risk factors of disease from non-coding sequence data. TraP outperforms leading methods in identifying non-coding variants that are pathogenic and is therefore a valuable tool for use in gene discovery and the interpretation of personal genomes., 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: 2016

40. Primer Part 1-The building blocks of epilepsy genetics

Author: Erin L. Heinzen, Heather C Mefford, and Ingo Helbig
Subjects: 0301 basic medicine, Population, Genomics, Biology, 03 medical and health sciences, Epilepsy, 0302 clinical medicine, Genetic variation, medicine, Humans, Genetic Predisposition to Disease, education, Genetics, education.field_of_study, Molecular Epidemiology, Massive parallel sequencing, Inheritance (genetic algorithm), Genetic Variation, Heritability, History, 20th Century, medicine.disease, 030104 developmental biology, Neurology, Genetic epidemiology, Neurology (clinical), 030217 neurology & neurosurgery
Abstract: This is the first of a two-part primer on the genetics of the epilepsies within the Genetic Literacy Series of the Genetics Commission of the International League Against Epilepsy. In Part 1, we cover the foundations of epilepsy genetics including genetic epidemiology and the range of genetic variants that can affect the risk for developing epilepsy. We discuss various epidemiologic study designs that have been applied to the genetics of the epilepsies including population studies, which provide compelling evidence for a strong genetic contribution in many epilepsies. We discuss genetic risk factors varying in size, frequency, inheritance pattern, effect size, and phenotypic specificity, and provide examples of how genetic risk factors within the various categories increase the risk for epilepsy. We end by highlighting trends in epilepsy genetics including the increasing use of massive parallel sequencing technologies.
Published: 2016

41. De Novo Mutations in SLC1A2 and CACNA1A Are Important Causes of Epileptic Encephalopathies

Author: Sophie Calvert, Amy L Schneider, Ruth Ottman, Mark I. Rees, Hugo Sampaio, Rikke S. Møller, Daniel H. Lowenstein, Stephen Petrou, Elliott H. Sherr, Erin L. Heinzen, Patrick Cossette, Seo-Kyung Chung, Julia Saykally, Gemma L. Carvill, Marina Nikanorova, Anthony G Marson, Michael P. Epstein, Matthew Zemel, David Goldstein, David Coman, Tracy A. Glauser, Samuel F. Berkovic, Jozef Gecz, Deepak Gill, Jacinta M McMahon, Ingrid E. Scheffer, Marvin Johnson, Norman Delanty, Terence J. O'Brien, Annapurna Poduri, William O. Pickrell, Tally Lerman-Sagie, Heather C Mefford, Jeremy L. Freeman, Georgina Hollingsworth, Mark A. Corbett, Andrew S. Allen, Patrick W. Carney, Evan E. Eichler, Lynette G. Sadleir, Ruben Kuzniecky, Slavé Petrovski, Candace T. Myers, Dennis J. Dlugos, and Amy Lacroix
Subjects: 0301 basic medicine, Adult, Male, Candidate gene, Adolescent, Disease, Biology, GTP-Binding Protein alpha Subunits, Gi-Go, medicine.disease_cause, Bioinformatics, N-Acetylglucosaminyltransferases, GNAO1, Article, Cohort Studies, 03 medical and health sciences, Glutamate Plasma Membrane Transport Proteins, 0302 clinical medicine, Seizures, Genotype, medicine, Genetics, Journal Article, Guanine Nucleotide Exchange Factors, Humans, Genetics(clinical), Allele, Genetics (clinical), Alleles, Mutation, Epilepsy, Genetic heterogeneity, Mosaicism, Infant, Newborn, Infant, Receptors, GABA-A, Genetic architecture, 030104 developmental biology, Excitatory Amino Acid Transporter 2, Child, Preschool, Female, Calcium Channels, 030217 neurology & neurosurgery
Abstract: Epileptic encephalopathies (EEs) are the most clinically important group of severe early-onset epilepsies. Next-generation sequencing has highlighted the crucial contribution of de novo mutations to the genetic architecture of EEs as well as to their underlying genetic heterogeneity. Our previous whole-exome sequencing study of 264 parent-child trios revealed more than 290 candidate genes in which only a single individual had a de novo variant. We sought to identify additional pathogenic variants in a subset (n = 27) of these genes via targeted sequencing in an unsolved cohort of 531 individuals with a diverse range of EEs. We report 17 individuals with pathogenic variants in seven of the 27 genes, defining a genetic etiology in 3.2% of this unsolved cohort. Our results provide definitive evidence that de novo mutations in SLC1A2 and CACNA1A cause specific EEs and expand the compendium of clinically relevant genotypes for GABRB3. We also identified EEs caused by genetic variants in ALG13, DNM1, and GNAO1 and report a mutation in IQSEC2. Notably, recurrent mutations accounted for 7/17 of the pathogenic variants identified. As a result of high-depth coverage, parental mosaicism was identified in two out of 14 cases tested with mutant allelic fractions of 5%-6% in the unaffected parents, carrying significant reproductive counseling implications. These results confirm that dysregulation in diverse cellular neuronal pathways causes EEs, and they will inform the diagnosis and management of individuals with these devastating disorders.
Published: 2016

42. Exome Sequencing and Functional Validation in Zebrafish Identify GTDC2 Mutations as a Cause of Walker-Warburg Syndrome

Author: Kevin V. Shianna, Jan M. Friedman, M. Chiara Manzini, Timothy W. Yu, Thomas M. Maynard, Abdel Karim Al-Qudah, Isabella Moroni, Erin L. Heinzen, Christine Stevens, R. Sean Hill, Marina Mora, Christopher A. Walsh, Jennifer N. Partlow, Vandana Gupta, Alan H. Beggs, Stacey Gabriel, Brenda J. Barry, Robin Clark, Dimira E. Tambunan, Wafaa Eyaid, Mustafa A. Salih, and Jacqueline Rodriguez
Subjects: Genetics, Mutation, Genetic heterogeneity, Glycosyltransferases, Walker-Warburg Syndrome, Biology, medicine.disease_cause, medicine.disease, biology.organism_classification, Report, medicine, Humans, Genetics(clinical), Exome, Walker–Warburg syndrome, Gene, Zebrafish, Genetics (clinical), Loss function, Exome sequencing
Abstract: Whole-exome sequencing (WES), which analyzes the coding sequence of most annotated genes in the human genome, is an ideal approach to studying fully penetrant autosomal-recessive diseases, and it has been very powerful in identifying disease-causing mutations even when enrollment of affected individuals is limited by reduced survival. In this study, we combined WES with homozygosity analysis of consanguineous pedigrees, which are informative even when a single affected individual is available, to identify genetic mutations responsible for Walker-Warburg syndrome (WWS), a genetically heterogeneous autosomal-recessive disorder that severely affects the development of the brain, eyes, and muscle. Mutations in seven genes are known to cause WWS and explain 50%–60% of cases, but multiple additional genes are expected to be mutated because unexplained cases show suggestive linkage to diverse loci. Using WES in consanguineous WWS-affected families, we found multiple deleterious mutations in GTDC2 (also known as AGO61). GTDC2’s predicted role as an uncharacterized glycosyltransferase is consistent with the function of other genes that are known to be mutated in WWS and that are involved in the glycosylation of the transmembrane receptor dystroglycan. Therefore, to explore the role of GTDC2 loss of function during development, we used morpholino-mediated knockdown of its zebrafish ortholog, gtdc2. We found that gtdc2 knockdown in zebrafish replicates all WWS features (hydrocephalus, ocular defects, and muscular dystrophy), strongly suggesting that GTDC2 mutations cause WWS.
Published: 2012

43. Exome Sequencing Followed by Large-Scale Genotyping Suggests a Limited Role for Moderately Rare Risk Factors of Strong Effect in Schizophrenia

Author: Herbert Y. Meltzer, Qian Zhao, Anu Putkonen, Eila Repo-Tiihonen, Peter B. Rosenquist, David Goldstein, Jessica M. Maia, Elizabeth T. Cirulli, Deborah L. Levy, Erin L. Heinzen, Min He, Curtis Gumbs, Dongliang Ge, Joseph P. McEvoy, Anna C. Need, Jari Tiihonen, Linda Hong, Kevin V. Shianna, Massimo Gennarelli, C. Ryan Campbell, and Tero Hallikainen
Subjects: Genotype, Molecular Sequence Data, Schizoaffective disorder, Genome-wide association study, Biology, Bioinformatics, Article, 03 medical and health sciences, 0302 clinical medicine, Risk Factors, medicine, Genetics, Humans, Exome, Genetic Predisposition to Disease, Genetics(clinical), Genotyping, Genetics (clinical), Exome sequencing, Finland, 030304 developmental biology, Genetic association, 0303 health sciences, Base Sequence, Sequence Analysis, DNA, medicine.disease, United States, 3. Good health, Schizophrenia, Sequence Alignment, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract: Schizophrenia is a severe psychiatric disorder with strong heritability and marked heterogeneity in symptoms, course, and treatment response. There is strong interest in identifying genetic risk factors that can help to elucidate the pathophysiology and that might result in the development of improved treatments. Linkage and genome-wide association studies (GWASs) suggest that the genetic basis of schizophrenia is heterogeneous. However, it remains unclear whether the underlying genetic variants are mostly moderately rare and can be identified by the genotyping of variants observed in sequenced cases in large follow-up cohorts or whether they will typically be much rarer and therefore more effectively identified by gene-based methods that seek to combine candidate variants. Here, we consider 166 persons who have schizophrenia or schizoaffective disorder and who have had either their genomes or their exomes sequenced to high coverage. From these data, we selected 5,155 variants that were further evaluated in an independent cohort of 2,617 cases and 1,800 controls. No single variant showed a study-wide significant association in the initial or follow-up cohorts. However, we identified a number of case-specific variants, some of which might be real risk factors for schizophrenia, and these can be readily interrogated in other data sets. Our results indicate that schizophrenia risk is unlikely to be predominantly influenced by variants just outside the range detectable by GWASs. Rather, multiple rarer genetic variants must contribute substantially to the predisposition to schizophrenia, suggesting that both very large sample sizes and gene-based association tests will be required for securely identifying genetic risk factors. © 2012 The American Society of Human Genetics.
Published: 2012
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44. Somatic Activation of AKT3 Causes Hemispheric Developmental Brain Malformations

Author: R. Sean Hill, Anthony D. Hill, Rameen Beroukhim, Gilad D. Evrony, L. Benjamin Hills, Brenda J. Barry, James J. Riviello, Peter McL. Black, Keith L. Ligon, Maria K. Lehtinen, Christopher A. Walsh, Princess C. Elhosary, Annapurna Poduri, Blaise F. D. Bourgeois, Erin L. Heinzen, Xuyu Cai, and A. James Barkovich
Subjects: Hemimegalencephaly, Somatic cell, Neuroscience(all), Neurogenesis, AKT1, Trisomy, Biology, medicine.disease_cause, Article, AKT3, 03 medical and health sciences, 0302 clinical medicine, medicine, Humans, Cerebrum, 030304 developmental biology, Genetics, 0303 health sciences, Mutation, Epilepsy, General Neuroscience, DEPDC5, Malformations of Cortical Development, Chromosomes, Human, Pair 1, Brain size, Cancer research, Proto-Oncogene Proteins c-akt, 030217 neurology & neurosurgery
Abstract: SummaryHemimegalencephaly (HMG) is a developmental brain disorder characterized by an enlarged, malformed cerebral hemisphere, typically causing epilepsy that requires surgical resection. We studied resected HMG tissue to test whether the condition might reflect somatic mutations affecting genes critical to brain development. We found that two out of eight HMG samples showed trisomy of chromosome 1q, which encompasses many genes, including AKT3, a gene known to regulate brain size. A third case showed a known activating mutation in AKT3 (c.49G→A, creating p.E17K) that was not present in the patient's blood cells. Remarkably, the E17K mutation in AKT3 is exactly paralogous to E17K mutations in AKT1 and AKT2 recently discovered in somatic overgrowth syndromes. We show that AKT3 is the most abundant AKT paralog in the brain during neurogenesis and that phosphorylated AKT is abundant in cortical progenitor cells. Our data suggest that somatic mutations limited to the brain could represent an important cause of complex neurogenetic disease.
Published: 2012

45. Postmortem Delay Has Minimal Effect on Brain RNA Integrity

Author: Kathleen A. Welsh-Bohmer, John F. Ervin, Erin L. Heinzen, David Goldstein, Christine M. Hulette, James R. Burke, Kenneth D. Cronin, and Mari H. Szymanski
Subjects: Male, Pathology, medicine.medical_specialty, Central nervous system, Hippocampus, Nerve Tissue Proteins, Biology, Postmortem Changes, Specimen Handling, Pathology and Forensic Medicine, Cellular and Molecular Neuroscience, Alzheimer Disease, Cortex (anatomy), Gene expression, medicine, Humans, Aged, Aged, 80 and over, Temporal cortex, Reverse Transcriptase Polymerase Chain Reaction, Brain, General Medicine, Human brain, Middle Aged, medicine.disease, medicine.anatomical_structure, Gene Expression Regulation, Neurology, RNA, Female, Neurology (clinical), Alzheimer's disease
Abstract: The Bryan Alzheimer Disease Research Center obtains postmortem human brain tissue from patients with Alzheimer disease (AD) and cognitively normal control subjects for molecular and genetic research programs. A growing body of research suggests that variations in gene transcript levels may contribute to the onset and progression of disease. Identifying how the regulation of gene expression may affect AD requires the use of high-quality mRNA from banked human brains. The present study was conducted to establish the quality and suitability of available banked brain tissue for future gene expression studies. We chose 32 AD cases with Braak stage IV, V, or VI. These AD cases were matched to 36 normal control cases by age and sex when possible. Multiple regions from each brain were sampled, including frontal cortex, temporal cortex, occipital cortex, and cerebellum. Hippocampus was also available for study from 14 control cases. A comparison of several antemortem and postmortem variables, such as postmortem interval, agonal state, ventricular cerebrospinal fluid pH, and cause of death were analyzed. RNA was isolated from at least 1 area from every brain and most brains yielded intact RNA from all regions tested. Analysis of the clinical variables did not reveal any features that correlated with the ability to recover intact mRNA. We conclude that undegraded mRNA may be isolated from most brain regions many hours postmortem and that neither the pH of ventricular fluid nor postmortem interval is predictive of mRNA integrity.
Published: 2007

46. The genetics of neuropsychiatric diseases: looking in and beyond the exome

Author: Benjamin M. Neale, David Goldstein, Erin L. Heinzen, Stephen F. Traynelis, and Andrew S. Allen
Subjects: Genetics, General Neuroscience, Mental Disorders, High-Throughput Nucleotide Sequencing, Biology, DNA sequencing, Mutation, Humans, Exome, Genetic Predisposition to Disease, Nervous System Diseases, Gene, De novo mutations, Exome sequencing, Gene Discovery, Neuropsychiatric disease, Genome-Wide Association Study
Abstract: Next-generation sequencing, which allows genome-wide detection of rare and de novo mutations, is transforming neuropsychiatric disease genetics through identifying on an unprecedented scale genes and protein-coding mutations that confer risk. Although understanding how regulatory variants influence risk remains a challenge, we are likely transitioning into a phase of neuropsychiatric disease genetics in which the rate-limiting step may no longer be gene discovery. Instead, the future will concentrate more on the biological and clinical translation of the torrent of specific risk mutations identified through next-generation sequencing. Here, we review the recent progress that resulted specifically from exome sequencing and emphasize the need for rigorous statistical evaluation of the expanding data sets, as well as expanded functional analysis of implicated proteins and mutations. Then, we introduce some of the expected opportunities and challenges investigators face when moving beyond the exome. Finally, we briefly highlight the challenge of deriving translational benefit from the progress in genetics.
Published: 2015

47. Somatic uniparental disomy of Chromosome 16p in hemimegalencephaly

Author: Kenneth D. Cronin, Gerald A. Grant, Nicole M. Walley, Andrew S. Allen, Erin L. Heinzen, Christine M. Hulette, Peter B. Crino, Mohamad A. Mikati, Nicole G. Griffin, Catherine Rehder, and Heather G. LaBreche
Subjects: Research Report, 0301 basic medicine, Genotype, Somatic cell, Buccal swab, Locus (genetics), Biology, Chromosomes, Genomic Imprinting, 03 medical and health sciences, 0302 clinical medicine, Chromosome 16, medicine, pachygyria, Humans, Alleles, Brain, Infant, Chromosome, hemimegalencephaly, DNA, General Medicine, DNA Methylation, Uniparental Disomy, medicine.disease, Molecular biology, Uniparental disomy, 030104 developmental biology, Child, Preschool, DNA methylation, Female, Genomic imprinting, Chromosomes, Human, Pair 16, 030217 neurology & neurosurgery
Abstract: Hemimegalencephaly (HME) is a heterogeneous cortical malformation characterized by enlargement of one cerebral hemisphere. Somatic variants in mammalian target of rapamycin (mTOR) regulatory genes have been implicated in some HME cases; however, ∼70% have no identified genetic etiology. Here, we screened two HME patients to identify disease-causing somatic variants. DNA from leukocytes, buccal swabs, and surgically resected brain tissue from two HME patients were screened for somatic variants using genome-wide genotyping arrays or sequencing of the protein-coding regions of the genome. Functional studies were performed to evaluate the molecular consequences of candidate disease-causing variants. Both HME patients evaluated were found to have likely disease-causing variants in DNA extracted from brain tissue but not in buccal swab or leukocyte DNA, consistent with a somatic mutational mechanism. In the first case, a previously identified disease-causing somatic single nucleotide in MTOR was identified. In the second case, we detected an overrepresentation of the alleles inherited from the mother on Chromosome 16 in brain tissue DNA only, indicative of somatic uniparental disomy (UPD) of the p-arm of Chromosome 16. Using methylation analyses, an imprinted locus on 16p spanning ZNF597 was identified, which results in increased expression of ZNF597 mRNA and protein in the brain tissue of the second case. Enhanced mTOR signaling was observed in tissue specimens from both patients. We speculate that overexpression of maternally expressed ZNF597 led to aberrant hemispheric development in the patient with somatic UPD of Chromosome 16p possibly through modulation of mTOR signaling.
Published: 2017

48. Determination of mycophenolic acid and its phenol glucuronide metabolite in human plasma and urine by high-performance liquid chromatography

Author: Kamonthip Wiwattanawongsa, Daniel C. Kemp, Philip C. Smith, Erin L. Heinzen, and Robert E. Dupuis
Subjects: Detection limit, Chromatography, Chemistry, Metabolite, Reproducibility of Results, General Chemistry, Urine, Mycophenolic Acid, Mycophenolate, Sensitivity and Specificity, High-performance liquid chromatography, chemistry.chemical_compound, Glucuronides, Blood plasma, Humans, Spectrophotometry, Ultraviolet, Glucuronide, Quantitative analysis (chemistry), Chromatography, High Pressure Liquid, Immunosuppressive Agents
Abstract: Simultaneous determination of mycophenolic acid (MPA) and mycophenolate phenol glucuronide (MPAG) in plasma and urine was accomplished by isocratic HPLC with UV detection. Plasma was simply deproteinated with acetonitrile and concentrated, whereas urine was diluted prior to analysis. Linearity was observed from 0.2 to 50 microg/ml for both MPA and MPAG in plasma and from 1 to 50 microg/ml of MPA and 5 to 2000 microg/ml MPAG in urine with extraction recovery from plasma greater than 70%. Detection limits using 0.25 ml plasma were 0.080 and 0.20 microg/ml for MPA and MPAG, respectively. The method is more rapid and simple than previous assays for MPA and MPAG in biological fluids from patients.
Published: 2001

49. SLC25A22 is a novel gene for migrating partial seizures in infancy

Author: Annapurna, Poduri, Erin L, Heinzen, Vida, Chitsazzadeh, Francesco Massimo, Lasorsa, P Christina, Elhosary, Christopher M, LaCoursiere, Emilie, Martin, Christopher J, Yuskaitis, Robert Sean, Hill, Kutay Deniz, Atabay, Brenda, Barry, Jennifer N, Partlow, Fahad A, Bashiri, Radwan M, Zeidan, Salah A, Elmalik, Mohammad M U, Kabiraj, Sanjeev, Kothare, Tommy, Stödberg, Amy, McTague, Manju A, Kurian, Ingrid E, Scheffer, A James, Barkovich, Ferdinando, Palmieri, Mustafa A, Salih, and Christopher A, Walsh
Subjects: Adult, Male, Genetic Linkage, Benign Neonatal, Clinical Sciences, Neurodegenerative, Mitochondrial Membrane Transport Proteins, Consanguinity, Clinical Research, Genetics, Humans, 2.1 Biological and endogenous factors, Exome, Aetiology, Pediatric, Epilepsy, Neurology & Neurosurgery, Human Genome, Infant, Newborn, Neurosciences, Infant, Newborn, Epilepsy, Benign Neonatal, Pedigree, Brain Disorders, Neurological, Female, Biotechnology
Abstract: ObjectiveTo identify a genetic cause for migrating partial seizures in infancy (MPSI).MethodsWe characterized a consanguineous pedigree with MPSI and obtained DNA from affected and unaffected family members. We analyzed single nucleotide polymorphism 500K data to identify regions with evidence of linkage. We performed whole exome sequencing and analyzed homozygous variants in regions of linkage to identify a candidate gene and performed functional studies of the candidate gene SLC25A22.ResultsIn a consanguineous pedigree with 2 individuals with MPSI, we identified 2 regions of linkage, chromosome 4p16.1-p16.3 and chromosome 11p15.4-pter. Using whole exome sequencing, we identified 8 novel homozygous variants in genes in these regions. Only 1 variant, SLC25A22 c.G328C, results in a change of a highly conserved amino acid (p.G110R) and was not present in control samples. SLC25A22 encodes a glutamate transporter with strong expression in the developing brain. We show that the specific G110R mutation, located in a transmembrane domain of the protein, disrupts mitochondrial glutamate transport.InterpretationWe have shown that MPSI can be inherited and have identified a novel homozygous mutation in SLC25A22 in the affected individuals. Our data strongly suggest that SLC25A22 is responsible for MPSI, a severe condition with few known etiologies. We have demonstrated that a combination of linkage analysis and whole exome sequencing can be used for disease gene discovery. Finally, as SLC25A22 had been implicated in the distinct syndrome of neonatal epilepsy with suppression bursts on electroencephalogram, we have expanded the phenotypic spectrum associated with SLC25A22.
Published: 2013

50. Using ERDS to Infer Copy-Number Variants in High-Coverage Genomes

Author: David Goldstein, Kimberly Pelak, Abanish Singh, Anna C. Need, Elizabeth K. Ruzzo, Min He, Curtis Gumbs, Qianqian Zhu, Mingfu Zhu, Erin L. Heinzen, Yujun Han, Elizabeth T. Cirulli, Kevin V. Shianna, Sheng Feng, Jessica M. Maia, and Dongliang Ge
Subjects: congenital, hereditary, and neonatal diseases and abnormalities, endocrine system diseases, DNA Copy Number Variations, Genotyping Techniques, Read depth, Computational biology, Biology, Validation Studies as Topic, High coverage, Genome, Article, 03 medical and health sciences, 0302 clinical medicine, Data sequences, mental disorders, Genetics, Humans, Genetics(clinical), Copy-number variation, Genetics (clinical), 030304 developmental biology, 0303 health sciences, Extramural, Genome, Human, Sequence Analysis, DNA, Gene deletion, 030217 neurology & neurosurgery, Algorithms, Gene Deletion
Abstract: Although there are many methods available for inferring copy-number variants (CNVs) from next-generation sequence data, there remains a need for a system that is computationally efficient but that retains good sensitivity and specificity across all types of CNVs. Here, we introduce a new method, estimation by read depth with single-nucleotide variants (ERDS), and use various approaches to compare its performance to other methods. We found that for common CNVs and high-coverage genomes, ERDS performs as well as the best method currently available (Genome STRiP), whereas for rare CNVs and high-coverage genomes, ERDS performs better than any available method. Importantly, ERDS accommodates both unique and highly amplified regions of the genome and does so without requiring separate alignments for calling CNVs and other variants. These comparisons show that for genomes sequenced at high coverage, ERDS provides a computationally convenient method that calls CNVs as well as or better than any currently available method.
Published: 2012

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