Epilepsy subtype-specific copy number burden observed in a genome-wide study of 17 458 subjects
Lisa‐Marie Niestroj, Eduardo Pérez‐Palma, Daniel P. Howrigan, Yadi Zhou, Feixiong Cheng, Elmo Saarentaus, Peter Nürnberg, Remi Stevelink, Mark J. Daly, Aarno Palotie, Dennis Lal, the Epi25 Collaborative, Yen‐Chen Anne Feng, Daniel P. Howrigan, Liam Abbott, Katherine Tashman, Felecia Cerrato, Dennis Lal, Claire Churchhouse, Namrata Gupta, Benjamin M. Neale, Samuel F. Berkovic, Holger Lerche, David B. Goldstein, 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 Dlugos, Ingrid E. Scheffer, Pasquale Striano, Catharine Freyer, Roland Krause, Patrick May, Kevin E. McKenna, Brigid M. Regan, Susannah T. Bellows, Costin Leu, Brigid M. Regan, Caitlin A. Bennett, Susannah T. Bellows, Esther C Johns, Alexandra MacDonald, Hannah Shilling, Rosemary Burgess, Dorien Weckhuysen, Melanie Bahlo, Terence J. O’Brien, Patrick Kwan, Slavé Petrovski, Marian Todaro, Sarah Weckhuysen, Hannah Stamberger, Peter De Jonghe, Chantal Depondt, Danielle M. Andrade, Tara Sadoway, Kelly Mo, Heinz Krestel, Sabina Gallati, Savvas 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
Abstract
Cytogenic testing is routinely applied in most neurological centres for severe paediatric epilepsies. However, which characteristics of copy number variants (CNVs) confer most epilepsy risk and which epilepsy subtypes carry the most CNV burden, have not been explored on a genome-wide scale. Here, we present the largest CNV investigation in epilepsy to date with 10 712 European epilepsy cases and 6746 ancestry-matched controls. Patients with genetic generalized epilepsy, lesional focal epilepsy, non-acquired focal epilepsy, and developmental and epileptic encephalopathy were included. All samples were processed with the same technology and analysis pipeline. All investigated epilepsy types, including lesional focal epilepsy patients, showed an increase in CNV burden in at least one tested category compared to controls. However, we observed striking differences in CNV burden across epilepsy types and investigated CNV categories. Genetic generalized epilepsy patients have the highest CNV burden in all categories tested, followed by developmental and epileptic encephalopathy patients. Both epilepsy types also show association for deletions covering genes intolerant for truncating variants. Genome-wide CNV breakpoint association showed not only significant loci for genetic generalized and developmental and epileptic encephalopathy patients but also for lesional focal epilepsy patients. With a 34-fold risk for developing genetic generalized epilepsy, we show for the first time that the established epilepsy-associated 15q13.3 deletion represents the strongest risk CNV for genetic generalized epilepsy across the whole genome. Using the human interactome, we examined the largest connected component of the genes overlapped by CNVs in the four epilepsy types. We observed that genetic generalized epilepsy and non-acquired focal epilepsy formed disease modules. In summary, we show that in all common epilepsy types, 1.5-3% of patients carry epilepsy-associated CNVs. The characteristics of risk CNVs vary tremendously across and within epilepsy types. Thus, we advocate genome-wide genomic testing to identify all disease-associated types of CNVs.