Genome-wide identification and phenotypic characterization of seizure-associated copy number variations in 741,075 individuals
Ludovica Montanucci, David Lewis‐Smith, Ryan L. Collins, Lisa‐Marie Niestroj, Shridhar Parthasarathy, Julie Xian, Shiva Ganesan, Marie Macnee, Tobias Brünger, Rhys H. Thomas, Michael E. Talkowski, Epi25 Collaborative, Joshua E. Motelow, Gundula Povysil, Ryan S. Dhindsa, Kate E. Stanley, Andrew S. Allen, David B. Goldstein, Yen‐Chen Anne Feng, Daniel P. Howrigan, Liam Abbott, Katherine Tashman, Felecia Cerrato, Caroline Cusick, Tarjinder Singh, Henrike Heyne, Andrea Byrnes, Claire Churchhouse, Nick Watts, Matthew Solomonson, Dennis Lal, Namrata Gupta, Benjamin M. Neale, Samuel F. Berkovic, Holger Lerche, Daniel H. Lowenstein, Gianpiero L. Cavalleri, Patrick Cossette, Chris Cotsapas, Peter De Jonghe, Tracy Dixon‐Salazar, Renzo Guerrini, Håkon Håkonarson, Erin L. Heinzen, Ingo Helbig, Patrick Kwan, Anthony G Marson, Slavé 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 E. McKenna, Brigid M. Regan, Caitlin A. Bennett, Stephanie L. Leech, Costin Leu, David Lewis‐Smith, Authors from individual Epi25 cohorts:, Australia: Melbourne (AUSAUS), Australia: Royal Melbourne (AUSRMB), Terence J. O’Brien, Marian Todaro, Belgium: Antwerp (BELATW), Hannah Stamberger, Belgium: Brussels (BELULB), Chantal Depondti, Canada: Andrade (CANUTN), Danielle M. Andrade, Quratulain Zulfiqar Ali, Tara Sadoway, Switzerland: Bern (CHEUBB), Heinz Krestel, André Schaller, Cyprus (CYPCYP), Savvas Papacostas, Ioanna Kousiappa, George A. Tanteles, Christou Yiolanda, Czech Republic: Prague (CZEMTH), Katalin Štěrbová, Markéta Vlčková, Lucie Sedláčková, Petra Laššuthová, Germany: Frankfurt/Marburg (DEUPUM), Karl Martin Klein, Felix Rosenow, Philipp S. Reif, Susanne Knake, Germany: Giessen (DEUUGS), Bernd A. Neubauer, Friedrich Zimprich, Martha Feucht
Abstract
Copy number variants (CNV) are established risk factors for neurodevelopmental disorders with seizures or epilepsy. With the hypothesis that seizure disorders share genetic risk factors, we pooled CNV data from 10,590 individuals with seizure disorders, 16,109 individuals with clinically validated epilepsy, and 492,324 population controls and identified 25 genome-wide significant loci, 22 of which are novel for seizure disorders, such as deletions at 1p36.33, 1q44, 2p21-p16.3, 3q29, 8p23.3-p23.2, 9p24.3, 10q26.3, 15q11.2, 15q12-q13.1, 16p12.2, 17q21.31, duplications at 2q13, 9q34.3, 16p13.3, 17q12, 19p13.3, 20q13.33, and reciprocal CNVs at 16p11.2, and 22q11.21. Using genetic data from additional 248,751 individuals with 23 neuropsychiatric phenotypes, we explored the pleiotropy of these 25 loci. Finally, in a subset of individuals with epilepsy and detailed clinical data available, we performed phenome-wide association analyses between individual CNVs and clinical annotations categorized through the Human Phenotype Ontology (HPO). For six CNVs, we identified 19 significant associations with specific HPO terms and generated, for all CNVs, phenotype signatures across 17 clinical categories relevant for epileptologists. This is the most comprehensive investigation of CNVs in epilepsy and related seizure disorders, with potential implications for clinical practice.