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1. Response to second treatment after initial failed treatment in a multicenter prospective infantile spasms cohort

Author

Knupp, Kelly G, Leister, Erin, Coryell, Jason, Nickels, Katherine C, Ryan, Nicole, Juarez‐Colunga, Elizabeth, Gaillard, William D, Mytinger, John R, Berg, Anne T, Millichap, John, Nordli, Douglas R, Joshi, Sucheta, Shellhaas, Renée A, Loddenkemper, Tobias, Dlugos, Dennis, Wirrell, Elaine, Sullivan, Joseph, Hartman, Adam L, Kossoff, Eric H, Grinspan, Zachary M, Hamikawa, Lorie, and Consortium, the Pediatric Epilepsy Research

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Pediatric, Clinical Research, Clinical Trials and Supportive Activities, 6.1 Pharmaceuticals, Evaluation of treatments and therapeutic interventions, Adrenocorticotropic Hormone, Anticonvulsants, Cohort Studies, Female, Humans, Infant, Male, Spasms, Infantile, Treatment Failure, Vigabatrin, Infantile spasms, Adrenocorticotropic hormone, Second-line treatment, Pediatric Epilepsy Research Consortium, Neurosciences, Neurology & Neurosurgery, Clinical sciences
Abstract

ObjectiveInfantile spasms (IS) represent a severe epileptic encephalopathy presenting in the first 2 years of life. Recommended first-line therapies (hormonal therapy or vigabatrin) often fail. We evaluated response to second treatment for IS in children in whom the initial therapy failed to produce both clinical remission and electrographic resolution of hypsarhythmia and whether time to treatment was related to outcome.MethodsThe National Infantile Spasms Consortium established a multicenter, prospective database enrolling infants with new diagnosis of IS. Children were considered nonresponders to first treatment if there was no clinical remission or persistence of hypsarhythmia. Treatment was evaluated as hormonal therapy (adrenocorticotropic hormone [ACTH] or oral corticosteroids), vigabatrin, or "other." Standard treatments (hormonal and vigabatrin) were compared to all other nonstandard treatments. We compared response rates using chi-square tests and multivariable logistic regression models.ResultsOne hundred eighteen infants were included from 19 centers. Overall response rate to a second treatment was 37% (n = 44). Children who received standard medications with differing mechanisms for first and second treatment had higher response rates than other sequences (27/49 [55%] vs. 17/69 [25%], p < 0.001). Children receiving first treatment within 4 weeks of IS onset had a higher response rate to second treatment than those initially treated later (36/82 [44%] vs. 8/34 [24%], p = 0.040).SignificanceGreater than one third of children with IS will respond to a second medication. Choosing a standard medication (ACTH, oral corticosteroids, or vigabatrin) that has a different mechanism of action appears to be more effective. Rapid initial treatment increases the likelihood of response to the second treatment.

Published
2016

2. Copy number variant analysis from exome data in 349 patients with epileptic encephalopathy

Author

Allen, Andrew S, Berkovic, Samuel F, Coe, Bradley P, Cook, Joseph, Cossette, Patrick, Delanty, Norman, Dlugos, Dennis, Eichler, Evan E, Epstein, Michael P, Glauser, Tracy, Goldstein, David B, Heinzen, Erin L, Johnson, Michael R, Krumm, Nik, Kuzniecky, Ruben, Lowenstein, Daniel H, Marson, Anthony G, Mefford, Heather C, Nelson, Ben, Esmaeeli Nieh, Sahar, O'Brien, Terence J, Ottman, Ruth, Petrou, Stephen, Petrovski, Slavé, Poduri, Annapurna, Raja, Archana, Ruzzo, Elizabeth K, Scheffer, Ingrid E, Sherr, Elliott, Abou‐Khalil, Bassel, Alldredge, Brian K, Andermann, Eva, Andermann, Frederick, Amron, Dina, Bautista, Jocelyn F, Boro, Alex, Cascino, Gregory, Consalvo, Damian, Crumrine, Patricia, Devinsky, Orrin, Fiol, Miguel, Fountain, Nathan B, French, Jacqueline, Friedman, Daniel, Geller, Eric B, Glynn, Simon, Haut, Sheryl R, Hayward, Jean, Helmers, Sandra L, Joshi, Sucheta, Kanner, Andres, Kirsch, Heidi E, Knowlton, Robert C, Kossoff, Eric H, Kuperman, Rachel, McGuire, Shannon M, Motika, Paul V, Novotny, Edward J, Paolicchi, Juliann M, Parent, Jack, Park, Kristen, Shellhaas, Renée A, Shih, Jerry J, Singh, Rani, Sirven, Joseph, Smith, Michael C, Sullivan, Joe, Thio, Liu Lin, Venkat, Anu, Vining, Eileen PG, Von Allmen, Gretchen K, Weisenberg, Judith L, Widdess‐Walsh, Peter, and Winawer, Melodie R

Subjects
Biomedical and Clinical Sciences, Neurosciences, Clinical Sciences, Neurodegenerative, Genetics, Intellectual and Developmental Disabilities (IDD), Epilepsy, Pediatric, Clinical Research, Brain Disorders, Human Genome, Aetiology, 2.1 Biological and endogenous factors, Adult, Child, Preschool, Cohort Studies, DNA Copy Number Variations, Exome, Female, Humans, Infant, Infant, Newborn, Lennox Gastaut Syndrome, Male, Parents, Sequence Analysis, DNA, Spasms, Infantile, Epilepsy Phenome/Genome Project Epi4K Consortium, Neurology & Neurosurgery, Clinical sciences
Abstract

Infantile spasms (IS) and Lennox-Gastaut syndrome (LGS) are epileptic encephalopathies characterized by early onset, intractable seizures, and poor developmental outcomes. De novo sequence mutations and copy number variants (CNVs) are causative in a subset of cases. We used exome sequence data in 349 trios with IS or LGS to identify putative de novo CNVs. We confirm 18 de novo CNVs in 17 patients (4.8%), 10 of which are likely pathogenic, giving a firm genetic diagnosis for 2.9% of patients. Confirmation of exome-predicted CNVs by array-based methods is still required due to false-positive rates of prediction algorithms. Our exome-based results are consistent with recent array-based studies in similar cohorts and highlight novel candidate genes for IS and LGS.

Published
2015

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

Author

Appenzeller, Silke, Balling, Rudi, Barisic, Nina, Baulac, Stéphanie, Caglayan, Hande, Craiu, Dana, De Jonghe, Peter, Depienne, Christel, Dimova, Petia, Djémié, Tania, Gormley, Padhraig, Guerrini, Renzo, Helbig, Ingo, Hjalgrim, Helle, Hoffman-Zacharska, Dorota, Jähn, Johanna, Klein, Karl Martin, Koeleman, Bobby, Komarek, Vladimir, Krause, Roland, Kuhlenbäumer, Gregor, Leguern, Eric, Lehesjoki, Anna-Elina, Lemke, Johannes R, Lerche, Holger, Linnankivi, Tarja, Marini, Carla, May, Patrick, Møller, Rikke S, Muhle, Hiltrud, Pal, Deb, Palotie, Aarno, Pendziwiat, Manuela, Robbiano, Angela, Roelens, Filip, Rosenow, Felix, Selmer, Kaja, Serratosa, Jose M, Sisodiya, Sanjay, Stephani, Ulrich, Sterbova, Katalin, Striano, Pasquale, Suls, Arvid, Talvik, Tiina, von Spiczak, Sarah, Weber, Yvonne, Weckhuysen, Sarah, Zara, Federico, Abou-Khalil, Bassel, Alldredge, Brian K, Andermann, Eva, Andermann, Frederick, Amron, Dina, Bautista, Jocelyn F, Berkovic, Samuel F, Bluvstein, Judith, Boro, Alex, Cascino, Gregory, Consalvo, Damian, Crumrine, Patricia, Devinsky, Orrin, Dlugos, Dennis, Epstein, Michael P, Fiol, Miguel, Fountain, Nathan B, French, Jacqueline, Friedman, Daniel, Geller, Eric B, Glauser, Tracy, Glynn, Simon, Haas, Kevin, Haut, Sheryl R, Hayward, Jean, Helmers, Sandra L, Joshi, Sucheta, Kanner, Andres, Kirsch, Heidi E, Knowlton, Robert C, Kossoff, Eric H, Kuperman, Rachel, Kuzniecky, Ruben, Lowenstein, Daniel H, McGuire, Shannon M, Motika, Paul V, Novotny, Edward J, Ottman, Ruth, Paolicchi, Juliann M, Parent, Jack, Park, Kristen, Poduri, Annapurna, Sadleir, Lynette, Scheffer, Ingrid E, Shellhaas, Renée A, Sherr, Elliott, Shih, Jerry J, Singh, Rani, Sirven, Joseph, Smith, Michael C, Sullivan, Joe, and Thio, Liu Lin

Subjects
Genetics, Pediatric, Neurosciences, Epilepsy, Brain Disorders, Neurodegenerative, 2.1 Biological and endogenous factors, Aetiology, Cohort Studies, Dynamin I, Exome, Fatty Acid Synthase, Type I, Female, Gene Regulatory Networks, Humans, Infant, Newborn, Lennox Gastaut Syndrome, Male, Mutation, Protein Interaction Maps, Receptors, GABA-B, Ryanodine Receptor Calcium Release Channel, Spasms, Infantile, Synaptic Transmission, EuroEPINOMICS-RES Consortium, Epilepsy Phenome/Genome Project, Epi4K Consortium, Biological Sciences, Medical and Health Sciences, Genetics & Heredity
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 novo mutations, including de novo mutations in DNM1 in five individuals and de novo 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 novo mutations in epileptic encephalopathy probands compared to the general population using a likelihood analysis (p = 8.2 × 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 novo 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
2014

4. The epilepsy phenome/genome project.

Author

EPGP Collaborative, Abou-Khalil, Bassel, Alldredge, Brian, Bautista, Jocelyn, Berkovic, Sam, Bluvstein, Judith, Boro, Alex, Cascino, Gregory, Consalvo, Damian, Cristofaro, Sabrina, Crumrine, Patricia, Devinsky, Orrin, Dlugos, Dennis, Epstein, Michael, Fahlstrom, Robyn, Fiol, Miguel, Fountain, Nathan, Fox, Kristen, French, Jacqueline, Freyer Karn, Catharine, Friedman, Daniel, Geller, Eric, Glauser, Tracy, Glynn, Simon, Haas, Kevin, Haut, Sheryl, Hayward, Jean, Helmers, Sandra, Joshi, Sucheta, Kanner, Andres, Kirsch, Heidi, Knowlton, Robert, Kossoff, Eric, Kuperman, Rachel, Kuzniecky, Ruben, Lowenstein, Daniel, McGuire, Shannon, Motika, Paul, Nesbitt, Gerard, Novotny, Edward, Ottman, Ruth, Paolicchi, Juliann, Parent, Jack, Park, Kristen, Poduri, Annapurna, Risch, Neil, Sadleir, Lynette, Scheffer, Ingrid, Shellhaas, Renee, Sherr, Elliott, Shih, Jerry J, Shinnar, Shlomo, Singh, Rani, Sirven, Joseph, Smith, Michael, Sullivan, Joe, Thio, Liu Lin, Venkat, Anu, Vining, Eileen, von Allmen, Gretchen, Weisenberg, Judith, Widdess-Walsh, Peter, and Winawer, Melodie

Subjects
EPGP Collaborative, Humans, Epilepsy, Oligonucleotide Array Sequence Analysis, Retrospective Studies, Genetic Research, Genotype, Phenotype, Research Design, Information Management, Clinical Research, Neurodegenerative, Neurosciences, Brain Disorders, Genetics, 2.1 Biological and endogenous factors, Aetiology, Neurological, Statistics, Clinical Sciences, Statistics & Probability
Abstract

BackgroundEpilepsy is a common neurological disorder that affects approximately 50 million people worldwide. Both risk of epilepsy and response to treatment partly depend on genetic factors, and gene identification is a promising approach to target new prediction, treatment, and prevention strategies. However, despite significant progress in the identification of genes causing epilepsy in families with a Mendelian inheritance pattern, there is relatively little known about the genetic factors responsible for common forms of epilepsy and so-called epileptic encephalopathies. Study design The Epilepsy Phenome/Genome Project (EPGP) is a multi-institutional, retrospective phenotype-genotype study designed to gather and analyze detailed phenotypic information and DNA samples on 5250 participants, including probands with specific forms of epilepsy and, in a subset, parents of probands who do not have epilepsy.ResultsEPGP is being executed in four phases: study initiation, pilot, study expansion/establishment, and close-out. This article discusses a number of key challenges and solutions encountered during the first three phases of the project, including those related to (1) study initiation and management, (2) recruitment and phenotyping, and (3) data validation. The study has now enrolled 4223 participants.ConclusionsEPGP has demonstrated the value of organizing a large network into cores with specific roles, managed by a strong Administrative Core that utilizes frequent communication and a collaborative model with tools such as study timelines and performance-payment models. The study also highlights the critical importance of an effective informatics system, highly structured recruitment methods, and expert data review.

Published
2013

5. Application of rare variant transmission disequilibrium tests to epileptic encephalopathy trio sequence data

Author

Allen, Andrew S, Berkovic, Samuel F, Bridgers, Joshua, Cossette, Patrick, Dlugos, Dennis, Epstein, Michael P, Glauser, Tracy, Goldstein, David B, Heinzen, Erin L, Jiang, Yu, Johnson, Michael R, Kuzniecky, Ruben, Lowenstein, Daniel H, Marson, Anthony G, Mefford, Heather C, O'Brien, Terence J, Ottman, Ruth, Petrou, Steven, Petrovski, Slave, Poduri, Annapurna, Ren, Zhong, Scheffer, Ingrid E, Sherr, Elliott, Wang, Quanli, Balling, Rudi, Barisic, Nina, Baulac, Stephanie, Caglayan, Hande, Craiu, Dana, De Jonghe, Peter, Depienne, Christel, Guerrini, Renzo, Helbig, Ingo, Hjalgrim, Helle, Hoffman-Zacharska, Dorota, Jaehn, Johanna, Klein, Karl Martin, Koeleman, Bobby, Komarek, Vladimir, Krause, Roland, Leguern, Eric, Lehesjoki, Anna-Elina, Lemke, Johannes R, Lerche, Holger, Linnankivi, Tarja, Marini, Carla, May, Patrick, Moller, Rikke S, Muhle, Hiltrud, Pal, Deb, Palotie, Aarno, Rosenow, Felix, Selmer, Kaja, Serratosa, Jose M, Sisodiya, Sanjay, Stephani, Ulrich, Sterbova, Katalin, Striano, Pasquale, Suls, Arvid, Talvik, Tiina, von Spiczak, Sarah, Weber, Yvonne, Weckhuysen, Sarah, Zara, Federico, Abou-Khalil, Bassel, Alldredge, Brian K, Amrom, Dina, Andermann, Eva, Andermann, Frederick, Bautista, Jocelyn F, Bluvstein, Judith, Cascino, Gregory D, Consalvo, Damian, Crumrine, Patricia, Devinsky, Orrin, Fiol, Miguel E, Fountain, Nathan B, French, Jacqueline, Friedman, Daniel, Haas, Kevin, Haut, Sheryl R, Hayward, Jean, Joshi, Sucheta, Kanner, Andres, Kirsch, Heidi E, Kossoff, Eric H, Kuperman, Rachel, McGuire, Shannon M, Motika, Paul V, Novotny, Edward J, Paolicchi, Juliann M, Parent, Jack, Park, Kristen, Shellhaas, Renee A, Sirven, Joseph, Smith, Michael C, Sullivan, Joseph, Thio, Liu Lin, Venkat, Anu, Vining, Eileen PG, Von Allmen, Gretchen K, Weisenberg, Judith L, Widdess-Walsh, Peter, Winawer, Melodie R, Consortium, Epi4K, Consortium, EuroEPINOMICS-RES, Project, Epilepsy Phenome Genome, Epi4K Consortium, EuroEPINOMICS- RES Consortium, and Epilepsy Phenome Genome Project

Subjects
0301 basic medicine, Linkage disequilibrium, medicine.medical_specialty, genetic structures, Population, Disequilibrium, Short Report, Genome-wide association study, Biology, Bioinformatics, Linkage Disequilibrium, 03 medical and health sciences, 0302 clinical medicine, Gene Frequency, Epilepsy Phenome/Genome Project, medicine, Genetics, Journal Article, Humans, Genetics(clinical), Genetic Predisposition to Disease, education, Genetics (clinical), education.field_of_study, Polymorphism, Genetic, Lennox Gastaut Syndrome, Infant, Transmission disequilibrium test, medicine.disease, Multicenter Study, Chemistry, 030104 developmental biology, Medical genetics, Human medicine, medicine.symptom, Spasms, Infantile, 030217 neurology & neurosurgery, Lennox–Gastaut syndrome, Genome-Wide Association Study
Abstract

The classic epileptic encephalopathies, including infantile spasms (IS) and Lennox-Gastaut syndrome (LGS), are severe seizure disorders that usually arise sporadically. De novo variants in genes mainly encoding ion channel and synaptic proteins have been found to account for over 15% of patients with IS or LGS. The contribution of autosomal recessive genetic variation, however, is less well understood. We implemented a rare variant transmission disequilibrium test (TDT) to search for autosomal recessive epileptic encephalopathy genes in a cohort of 320 outbred patient-parent trios that were generally prescreened for rare metabolic disorders. In the current sample, our rare variant transmission disequilibrium test did not identify individual genes with significantly distorted transmission over expectation after correcting for the multiple tests. While the rare variant transmission disequilibrium test did not find evidence of a role for individual autosomal recessive genes, our current sample is insufficiently powered to assess the overall role of autosomal recessive genotypes in an outbred epileptic encephalopathy population.

Published
2017

6. Response to Treatment in a Prospective National Infantile Spasms Cohort

Author

Knupp, Kelly G., Coryell, Jason, Nickels, Katherine C., Ryan, Nicole, Leister, Erin, Loddenkemper, Tobias, Grinspan, Zachary, Hartman, Adam L., Kossoff, Eric H., Gaillard, William D., Mytinger, John R., Joshi, Sucheta, Shellhaas, Renée A., Sullivan, Joseph, Dlugos, Dennis, Hamikawa, Lorie, Berg, Anne T., Millichap, John, Nordli, Douglas R., and Wirrell, Elaine

Subjects
Male, Administration, Oral, Infant, Article, United States, Vigabatrin, Cohort Studies, Adrenocorticotropic Hormone, Adrenal Cortex Hormones, Risk Factors, Child, Preschool, Prevalence, Humans, Anticonvulsants, Female, Prospective Studies, Spasms, Infantile
Abstract

Infantile spasms are seizures associated with a severe epileptic encephalopathy presenting in the first 2 years of life, and optimal treatment continues to be debated. This study evaluates early and sustained response to initial treatments and addresses both clinical remission and electrographic resolution of hypsarrhythmia. Secondarily, it assesses whether response to treatment differs by etiology or developmental status.The National Infantile Spasms Consortium established a multicenter, prospective database enrolling infants with new diagnosis of infantile spasms. Children were considered responders if there was clinical remission and resolution of hypsarrhythmia that was sustained at 3 months after first treatment initiation. Standard treatments of adrenocorticotropic hormone (ACTH), oral corticosteroids, and vigabatrin were considered individually, and all other nonstandard therapies were analyzed collectively. Developmental status and etiology were assessed. We compared response rates by treatment group using chi-square tests and multivariate logistic regression models.Two hundred thirty infants were enrolled from 22 centers. Overall, 46% of children receiving standard therapy responded, compared to only 9% who responded to nonstandard therapy (p 0.001). Fifty-five percent of infants receiving ACTH as initial treatment responded, compared to 39% for oral corticosteroids, 36% for vigabatrin, and 9% for other (p 0.001). Neither etiology nor development significantly modified the response pattern by treatment group.Response rate varies by treatment choice. Standard therapies should be considered as initial treatment for infantile spasms, including those with impaired development or known structural or genetic/metabolic etiology. ACTH appeared to be more effective than other standard therapies.

Published
2016

7. Copy number variant analysis from exome data in 349 patients with epileptic encephalopathy

Author

Allen, Andrew S., Berkovic, Samuel F., Coe, Bradley P., Cook, Joseph, Cossette, Patrick, Delanty, Norman, Dlugos, Dennis, Eichler, Evan E., Epstein, Michael P., Glauser, Tracy, Goldstein, David B., Heinzen, Erin L., Johnson, Michael R., Krumm, Nik, Kuzniecky, Ruben, Lowenstein, Daniel H., Marson, Anthony G., Mefford, Heather C., Nelson, Ben, Esmaeeli Nieh, Sahar, O'Brien, Terence J., Ottman, Ruth, Petrou, Stephen, Petrovski, Slavé, Poduri, Annapurna, Raja, Archana, Ruzzo, Elizabeth K., Scheffer, Ingrid E., Sherr, Elliott, Abou‐Khalil, Bassel, Alldredge, Brian K., Andermann, Eva, Andermann, Frederick, Amron, Dina, Bautista, Jocelyn F., Boro, Alex, Cascino, Gregory, Consalvo, Damian, Crumrine, Patricia, Devinsky, Orrin, Fiol, Miguel, Fountain, Nathan B., French, Jacqueline, Friedman, Daniel, Geller, Eric B., Glynn, Simon, Haut, Sheryl R., Hayward, Jean, Helmers, Sandra L., Joshi, Sucheta, Kanner, Andres, Kirsch, Heidi E., Knowlton, Robert C., Kossoff, Eric H., Kuperman, Rachel, McGuire, Shannon M., Motika, Paul V., Novotny, Edward J., Paolicchi, Juliann M., Parent, Jack, Park, Kristen, Shellhaas, Renée A., Shih, Jerry J., Singh, Rani, Sirven, Joseph, Smith, Michael C., Sullivan, Joe, Thio, Liu Lin, Venkat, Anu, Vining, Eileen P.G., Von Allmen, Gretchen K., Weisenberg, Judith L., Widdess‐Walsh, Peter, Winawer, Melodie R., and Wellcome Trust

Subjects
Parents, Male, Epilepsy Phenome/Genome Project Epi4K Consortium, Neurodegenerative, Bioinformatics, Infantile, Spasms, Cohort Studies, Epilepsy, 0302 clinical medicine, 2.1 Biological and endogenous factors, Exome, Copy-number variation, Aetiology, Child, Exome sequencing, Genetics, Pediatric, 0303 health sciences, Neurology, Child, Preschool, Female, Brief Communications, Spasms, Infantile, Sequence Analysis, Adult, DNA Copy Number Variations, Intellectual and Developmental Disabilities (IDD), Clinical Sciences, Copy number analysis, Phenome, Biology, Brief Communication, 03 medical and health sciences, Clinical Research, mental disorders, medicine, Humans, Preschool, 030304 developmental biology, Neurology & Neurosurgery, Lennox Gastaut Syndrome, Human Genome, Infant, Newborn, Neurosciences, Infant, 1103 Clinical Sciences, Sequence Analysis, DNA, DNA, medicine.disease, Newborn, Brain Disorders, Human genome, Neurology (clinical), 1109 Neurosciences, 030217 neurology & neurosurgery, Lennox–Gastaut syndrome
Abstract

The epileptic encephalopathies (EEs) are a devastating group of epilepsies in which epileptic activity and seizures contribute to cognitive impairment or regression.1 Most EEs begin in infancy or early childhood and are associated with poor developmental outcome. Although the cause is unknown in the majority of cases, recent studies confirm that de novo mutations and copy number variants (CNVs) play an important role.2, 3 We recently reported exome sequencing data in 264 parent–proband trios with infantile spasms (n = 149) or Lennox–Gastaut syndrome (LGS; n = 115) without syndromic features or magnetic resonance imaging (MRI) abnormalities from the Epilepsy Phenome/Genome Project (EPGP) cohort, identifying likely pathogenic, de novo sequence changes in >10% of patients.2 Here we report results of copy number analysis derived from the exome data of this cohort and 85 additional patients to further elucidate the genetic architecture of these paradigmatic EEs. Our exome‐based CNV calling yields similar results to array‐based studies for confirmed, de novo, likely pathogenic CNVs.

Published
2015

8. Association of ultra-rare coding variants with genetic generalized epilepsy: A case–control whole exome sequencing study

Author

Koko, M., Motelow, J. E., Stanley, K. E., Bobbili, D. R., Dhindsa, R. S., May, P., Alldredge, B. K., Allen, A. S., Altmuller, J., Amrom, D., Andermann, E., Auce, P., Avbersek, A., Baulac, S., Bautista, J. F., Becker, F., Bellows, S. T., Berghuis, B., Berkovic, S. F., Bluvstein, J., Boro, A., Bridgers, J., Burgess, R., Caglayan, H., Cascino, G. D., Cavalleri, G. L., Chung, S. -K., Cieuta-Walti, C., Cloutier, V., Consalvo, D., Cossette, P., Crumrine, P., Delanty, N., Depondt, C., Desbiens, R., Devinsky, O., Dlugos, D., Epstein, M. P., Everett, K., Fiol, M., Fountain, N. B., Francis, B., French, J., Freyer, C., Friedman, D., Gambardella, A., Geller, E. B., Girard, S., Glauser, T., Glynn, S., Goldstein, D. B., Gravel, M., Haas, K., Haut, S. R., Heinzen, E. L., Helbig, I., Hildebrand, M. S., Johnson, M. R., Jorgensen, A., Joshi, S., Kanner, A., Kirsch, H. E., Klein, K. M., Knowlton, R. C., Koeleman, B. P. C., Kossoff, E. H., Krause, R., Krenn, M., Kunz, W. S., Kuzniecky, R., Langley, S. R., Leguern, E., Lehesjoki, A. -E., Lerche, H., Leu, C., Lortie, A., Lowenstein, D. H., Marson, A. G., Mebane, C., Mefford, H. C., Meloche, C., Moreau, C., Motika, P. V., Muhle, H., Moller, R. S., Nabbout, R., Nguyen, D. K., Nikanorova, M., Novotny, E. J., Nurnberg, P., Ottman, R., O'Brien, T. J., Paolicchi, J. M., Parent, J. M., Park, K., Peter, S., Petrou, S., Petrovski, S., Pickrell, W. O., Poduri, A., Radtke, R. A., Rees, M. I., Regan, B. M., Ren, Z., Sadleir, L. G., Sander, J. W., Sander, T., Scheffer, I. E., Schubert, J., Shellhaas, R. A., Sherr, E. H., Shih, J. J., Shinnar, S., Sills, G. J., Singh, R. K., Siren, A., Sirven, J., Sisodiya, S. M., Smith, M. C., Sonsma, A. C. M., Striano, P., Sullivan, J., Thio, L. L., Thomas, R. H., Venkat, A., Vining, E. P. G., Von Allmen, G. K., Wang, Q., Weber, Y. G., Weckhuysen, S., Weisenberg, J. L., Widdess-Walsh, P., Winawer, M. R., Wolking, S., Zara, F., Zimprich, F., Canadian Epilepsy Network, Epi4K Consortium, Epilepsy Phenome/Genome Project, EpiPGX Consortium, EuroEPINOMICS-CoGIE Consortium, Department of Medical and Clinical Genetics, Medicum, Fonds National de la Recherche - FnR [sponsor], Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Peter, Sarah, Petrou, Steven, Petrovski, Slavé, Pickrell, William O., Poduri, Annapurna, Radtke, Rodney A., Rees, Mark I., Regan, Brigid M., Ren, Zhong, Sadleir, Lynette G., Alldredge, Brian K., Sander, Josemir W., Sander, Thomas, Scheffer, Ingrid E., Schubert, Julian, Shellhaas, Renée A., Sherr, Elliott H., Shih, Jerry J., Shinnar, Shlomo, Sills, Graeme J., Singh, Rani K., Allen, Andrew S., Siren, Auli, Sirven, Joseph, Sisodiya, Sanjay M., Smith, Michael C., Sonsma, Anja C. M., Striano, Pasquale, Sullivan, Joseph, Thio, Liu Lin, Thomas, Rhys H., Venkat, Anu, Altmüller, Janine, Vining, Eileen P. G., Von Allmen, Gretchen K., Wang, Quanli, Weber, Yvonne G., Weckhuysen, Sarah, Weisenberg, Judith L., Widdess-Walsh, Peter, Winawer, Melodie R., Wolking, Stefan, Zara, Federico, Amrom, Dina, Zimprich, Fritz, Andermann, Eva, Auce, Pauls, Avbersek, Andreja, Baulac, Stéphanie, Bautista, Jocelyn F., Becker, Felicitas, Bellows, Susannah T., Berghuis, Bianca, Berkovic, Samuel F., Bluvstein, Judith, Boro, Alex, Bridgers, Joshua, Burgess, Rosemary, Caglayan, Hande, Cascino, Gregory D., Cavalleri, Gianpiero L., Chung, Seo-Kyung, Cieuta-Walti, Cécile, Cloutier, Véronique, Consalvo, Damian, Cossette, Patrick, Crumrine, Patricia, Delanty, Norman, Depondt, Chantal, Desbiens, Richard, Devinsky, Orrin, Dlugos, Dennis, Epstein, Michael P., Everett, Kate, Fiol, Miguel, Fountain, Nathan B., Francis, Ben, French, Jacqueline, Freyer, Catharine, Friedman, Daniel, Gambardella, Antonio, Geller, Eric B., Girard, Simon, Glauser, Tracy, Glynn, Simon, Goldstein, David B., Gravel, Micheline, Haas, Kevin, Haut, Sheryl R., Heinzen, Erin L., Helbig, Ingo, Hildebrand, Michael S., Johnson, Michael R., Jorgensen, Andrea, Joshi, Sucheta, Kanner, Andres, Kirsch, Heidi E., Klein, Karl M., Knowlton, Robert C., Koeleman, Bobby P. C., Kossoff, Eric H., Krause, Roland, Krenn, Martin, Kunz, Wolfram S., Kuzniecky, Ruben, Langley, Sarah R., LeGuern, Eric, Lehesjoki, Anna-Elina, Lerche, Holger, Leu, Costin, Lortie, Anne, Lowenstein, Daniel H., Marson, Anthony G., Mebane, Caroline, Mefford, Heather C., Meloche, Caroline, Moreau, Claudia, Motika, Paul V., Muhle, Hiltrud, Møller, Rikke S., Nabbout, Rima, Nguyen, Dang K., Nikanorova, Marina, Novotny, Edward J., Nürnberg, Peter, Ottman, Ruth, O'Brien, Terence J., Paolicchi, Juliann M., Parent, Jack M., and Park, Kristen

Subjects
GABA receptors, Neurology [D14] [Human health sciences], Clinical Sciences, GABA(A) receptors, GABRG2, familial epilepsy, Article, Clinical Research, Receptors, Exome Sequencing, Genetics, 2.1 Biological and endogenous factors, Humans, GGE, Genetic Predisposition to Disease, sporadic epilepsy, EpiPGX Consortium, Aetiology, gamma-Aminobutyric Acid, GABAA receptors, Epi4K Consortium, Epilepsy, Neurology & Neurosurgery, Neurologie [D14] [Sciences de la santé humaine], Generalized, GABA-A, Prevention, Human Genome, Neurosciences, 1184 Genetics, developmental biology, physiology, 3112 Neurosciences, Receptors, GABA-A, EuroEPINOMICS-CoGIE Consortium, Neurology, Case-Control Studies, Epilepsy, Generalized, Canadian Epilepsy Network, Neurology (clinical), Genetics & genetic processes [F10] [Life sciences], 3111 Biomedicine, Human medicine, Génétique & processus génétiques [F10] [Sciences du vivant], Epilepsy Phenome/Genome Project
Abstract

ObjectiveWe aimed to identify genes associated with genetic generalized epilepsy (GGE) by combining large cohorts enriched with individuals with a positive family history. Secondarily, we set out to compare the association of genes independently with familial and sporadic GGE.MethodsWe performed a case-control whole exome sequencing study in unrelated individuals of European descent diagnosed with GGE (previously recruited and sequenced through multiple international collaborations) and ancestry-matched controls. The association of ultra-rare variants (URVs; in 18834 protein-coding genes) with epilepsy was examined in 1928 individuals with GGE (vs. 8578 controls), then separately in 945 individuals with familial GGE (vs. 8626 controls), and finally in 1005 individuals with sporadic GGE (vs. 8621 controls). We additionally examined the association of URVs with familial and sporadic GGE in two gene sets important for inhibitory signaling (19genes encoding γ-aminobutyric acid type A [GABAA ] receptors, 113genes representing the GABAergic pathway).ResultsGABRG2 was associated with GGE (p=1.8×10-5 ), approaching study-wide significance in familial GGE (p=3.0×10-6 ), whereas no gene approached a significant association with sporadic GGE. Deleterious URVs in the most intolerant subgenic regions in genes encoding GABAA receptors were associated with familial GGE (odds ratio [OR]=3.9, 95% confidence interval [CI]=1.9-7.8, false discovery rate [FDR]-adjusted p=.0024), whereas their association with sporadic GGE had marginally lower odds (OR=3.1, 95% CI=1.3-6.7, FDR-adjusted p=.022). URVs in GABAergic pathway genes were associated with familial GGE (OR=1.8, 95% CI=1.3-2.5, FDR-adjusted p=.0024) but not with sporadic GGE (OR=1.3, 95% CI=.9-1.9, FDR-adjusted p=.19).SignificanceURVs in GABRG2 are likely an important risk factor for familial GGE. The association of gene sets of GABAergic signaling with familial GGE is more prominent than with sporadic GGE.

Published
2022

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