Burden analysis of rare microdeletions suggests a strong impact of neurodevelopmental genes in genetic generalised epilepsies

Dennis Lal, Ann-Kathrin Ruppert, Holger Trucks, Herbert Schulz, Carolien G de Kovel, Dorothée Kasteleijn-Nolst Trenité, Anja C M Sonsma, Bobby P Koeleman, Dick Lindhout, Yvonne G Weber, Holger Lerche, Claudia Kapser, Christoph J Schankin, Wolfram S Kunz, Rainer Surges, Christian E Elger, Verena Gaus, Bettina Schmitz, Ingo Helbig, Hiltrud MuhleUlrich Stephani, Karl M Klein, Felix Rosenow, Bernd A Neubauer, Eva M Reinthaler, Fritz Zimprich, Martha Feucht, Rikke S Møller, Helle Hjalgrim, Peter De Jonghe, Arvid Suls, Wolfgang Lieb, Andre Franke, Konstantin Strauch, Christian Gieger, Claudia Schurmann, Ulf Schminke, Peter Nürnberg, Thomas Sander, EPICURE Consortium

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Genetic generalised epilepsy (GGE) is the most common form of genetic epilepsy, accounting for 20% of all epilepsies. Genomic copy number variations (CNVs) constitute important genetic risk factors of common GGE syndromes. In our present genome-wide burden analysis, large (≥ 400 kb) and rare (< 1%) autosomal microdeletions with high calling confidence (≥ 200 markers) were assessed by the Affymetrix SNP 6.0 array in European case-control cohorts of 1,366 GGE patients and 5,234 ancestry-matched controls. We aimed to: 1) assess the microdeletion burden in common GGE syndromes, 2) estimate the relative contribution of recurrent microdeletions at genomic rearrangement hotspots and non-recurrent microdeletions, and 3) identify potential candidate genes for GGE. We found a significant excess of microdeletions in 7.3% of GGE patients compared to 4.0% in controls (P = 1.8 x 10-7; OR = 1.9). Recurrent microdeletions at seven known genomic hotspots accounted for 36.9% of all microdeletions identified in the GGE cohort and showed a 7.5-fold increased burden (P = 2.6 x 10-17) relative to controls. Microdeletions affecting either a gene previously implicated in neurodevelopmental disorders (P = 8.0 x 10-18, OR = 4.6) or an evolutionarily conserved brain-expressed gene related to autism spectrum disorder (P = 1.3 x 10-12, OR = 4.1) were significantly enriched in the GGE patients. Microdeletions found only in GGE patients harboured a high proportion of genes previously associated with epilepsy and neuropsychiatric disorders (NRXN1, RBFOX1, PCDH7, KCNA2, EPM2A, RORB, PLCB1). Our results demonstrate that the significantly increased burden of large and rare microdeletions in GGE patients is largely confined to recurrent hotspot microdeletions and microdeletions affecting neurodevelopmental genes, suggesting a strong impact of fundamental neurodevelopmental processes in the pathogenesis of common GGE syndromes.

Original languageEnglish
Article numbere1005226
JournalPLOS Genetics
Issue number5
Number of pages21
Publication statusPublished - 2015

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