Developmental Biology - Epilepsy|
Linking Epilepsy to Genes
Genetic research was conducted on the largest ever group of people with epilepsy...
Researchers and patients from the Department of Medicine, Austin Health & Northern Health, University of Melbourne. were involved in the largest ever study of genetic sequences in people with epilepsy. The international research team published their results this week in the American Journal of Human Genetics. Involving almost 18,000 people worldwide, the research identified rare genetic variations associated with a higher risk of epilepsy.
The study found genetic links shared by both severe and less severe forms of the disease.
"There are approximately 50 million people across the world with epilepsy, a condition that causes repeated seizures due to excessive electrical activity in the brain," explains Sam Berkovic, Director, Department of Epilepsy at Austin Health, and Laureate Professor with the University of Melbourne.
"Epilepsy comes in a number of different forms ranging from less common variations such as developmental and epileptic encephalopathies that cause severe symptoms, to other, less severe forms such as genetic generalised epilepsy and non-acquired focal epilepsy that account for up to 40 per cent of cases.
"This research is important because the more we understand the genes that are linked to epilepsy, the better we can tailor treatments to reduce the symptoms and let patients live more active lives."
Sam Berkovic PhD, Director, Department of Epilepsy, University of Melbourne, Austin Health Center and Laureate Professor.
The study brought together more than 200 researchers from across the world to better understand the genetics of the disease. Researchers sequenced genes from 17,606 people from across 37 sites in Europe, North America, Australasia and Asia and found rare genetic variations that are associated with both severe and less severe forms of epilepsy.
The coordination of the clinical data occurred in Melbourne with the gene sequencing performed at the Broad Institute, Boston, led by Dr Benjamin Neale. 1370 patients from Austin Health and the University of Melbourne were part of the study, which was five times larger than any previous research looking at the gene sequencing of epilepsy patients.
"Genetic sequencing has significantly improved our understanding of the risk factors association with epilepsy in recent years. This study shows that more and less severe forms of the disease share similar genetic features, and the more we understand these features the better chance we have to personalise the care we give to patients.
"There are already plans in place to double the size of the study in the next year to further explore the significance of the genetic variations that are linked with epilepsy."
Sam Berkovic PhD.
Sequencing-based studies have identified novel risk genes associated with severe epilepsies and revealed an excess of rare deleterious variation in less-severe forms of epilepsy. To identify the shared and distinct ultra-rare genetic risk factors for different types of epilepsies, we performed a whole-exome sequencing (WES) analysis of 9,170 epilepsy-affected individuals and 8,436 controls of European ancestry. We focused on three phenotypic groups: severe developmental and epileptic encephalopathies (DEEs), 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; we saw the strongest enrichment in individuals with DEEs and the least strong in individuals with NAFE. Moreover, we found that inhibitory GABAA receptor genes were enriched for missense variants across all three classes of epilepsy, whereas 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 DEEs 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 lead associations; such genes included CACNA1G, EEF1A2, and GABRG2 for GGE and LGI1, TRIM3, and GABRG2 for NAFE. Our study, the largest epilepsy WES study to date, confirms a convergence in the genetics of severe and less-severe epilepsies associated with ultra-rare coding variation, and it highlights a ubiquitous role for GABAergic inhibition in epilepsy etiology.
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. OBrien, 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 t?rbová, Markéta Vl?ková, Lucie Sedlá?ková, Petra Lauthová, 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, Gerhard Kurlemann, 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 Barii?, 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 Yap?c?, Uluc Yis, P?nar Topaloglu, Bulent Kara, Dilsad Turkdogan, Asl? Gundogdu-Eken, Nerses Bebek, Sibel U?ur-??eri, Betül Baykan, Bar?? Salman, Garen Haryanyan, Emrah Yücesan, Ye?im Kesim, Çi?dem 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 and Benjamin M. Neale.
The authors gratefully thank the Epi25 principal investigators, local staff from individual cohorts, and all of the individuals with epilepsy who participated in the study for making possible this global collaboration and resource to advance epilepsy genetics research. This work is part of the Centers for Common Disease Genomics (CCDG) program, funded by the National Human Genome Research Institute (NHGRI) and the National Heart, Lung, and Blood Institute (NHLBI). CCDG research activities at the Broad Institute were supported by NHGRI grant UM1 HG008895. The Genome Sequencing Program efforts were also supported by NHGRI grant 5U01HG009088-02. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. A supplemental grant for Epi25 phenotyping was supported by Epi25 Clinical Phenotyping R03, National Institutes of Health (1R03NS108145-01), with D.H.L. and S.F.B. as the principal investigators. Additional funding sources and acknowledgment of individual case and control cohorts were listed in the Supplemental Data. We thank the Stanley Center for Psychiatric Research at the Broad Institute for supporting sequencing effort and control sample aggregation. The authors would like to thank the Discov-EHR collaboration of Geisinger Health System and Regeneron for providing exome variant data for comparison. We also thank Sali Farhan, Kyle Satterstrom, and Chai-Yen Chen for helpful discussions, Nick Watts and Matthew Solomonson for browser development, and the Hail team for analysis support.
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