Polygenic burden in focal and generalized epilepsies

Costin Leu, Remi Stevelink, Alexander W. Smith, Slavina B. Goleva, Masahiro Kanai, Lisa Ferguson, Ciaran Campbell, Yoichiro Kamatani, Yukinori Okada, Sanjay M. Sisodiya, Gianpiero L. Cavalleri, Bobby P.C. Koeleman, Holger Lerche, Lara Jehi, Lea K. Davis, Imad M. Najm, Aarno Palotie, Mark J. Daly, Robyn M. Busch, Dennis LalEpi25 Consortium

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4 Citations (Scopus)

Abstract

Rare genetic variants can cause epilepsy, and genetic testing has been widely adopted for severe, paediatric-onset epilepsies. The phenotypic consequences of common genetic risk burden for epilepsies and their potential future clinical applications have not yet been determined. Using polygenic risk scores (PRS) from a European-ancestry genome-wide association study in generalized and focal epilepsy, we quantified common genetic burden in patients with generalized epilepsy (GE-PRS) or focal epilepsy (FE-PRS) from two independent non-Finnish European cohorts (Epi25 Consortium, n = 5705; Cleveland Clinic Epilepsy Center, n = 620; both compared to 20 435 controls). One Finnish-ancestry population isolate (Finnish-ancestry Epi25, n = 449; compared to 1559 controls), two European-ancestry biobanks (UK Biobank, n = 383 656; Vanderbilt biorepository, n = 49 494), and one Japaneseancestry biobank (BioBank Japan, n = 168 680) were used for additional replications. Across 8386 patients with epilepsy and 622 212 population controls, we found and replicated significantly higher GE-PRS in patients with generalized epilepsy of European-ancestry compared to patients with focal epilepsy (Epi25: P = 1.64×10-15; Cleveland: P = 2.85×10-4; Finnish-ancestry Epi25: P = 1.80×10-4) or population controls (Epi25: P = 2.35×10-70; Cleveland: P = 1.43×10-7; Finnish-ancestry Epi25: P = 3.11×10-4; UK Biobank and Vanderbilt biorepository meta-analysis: P = 7.99×10-4). FE-PRS were significantly higher in patients with focal epilepsy compared to controls in the non-Finnish, non-biobank cohorts (Epi25: P = 5.74×10-19; Cleveland: P = 1.69×10-6). European ancestry-derived PRS did not predict generalized epilepsy or focal epilepsy in Japanese-ancestry individuals. Finally, we observed a significant 4.6-fold and a 4.5-fold enrichment of patients with generalized epilepsy compared to controls in the top 0.5% highest GE-PRS of the two non-Finnish European cohorts (Epi25: P = 2.60×10-15; Cleveland: P = 1.39×10-2). We conclude that common variant risk associated with epilepsy is significantly enriched in multiple cohorts of patients with epilepsy compared to controls-in particular for generalized epilepsy. As sample sizes and PRS accuracy continue to increase with further common variant discovery, PRS could complement established clinical biomarkers and augment genetic testing for patient classification, comorbidity research, and potentially targeted treatment.

Original languageEnglish
Pages (from-to)3473-3481
Number of pages9
JournalBrain
Volume142
Issue number11
DOIs
Publication statusPublished - 1 Nov 2019

Keywords

  • Common variant risk
  • Epilepsy
  • Genetic generalized epilepsy
  • Genetics

Cite this

Leu, C., Stevelink, R., Smith, A. W., Goleva, S. B., Kanai, M., Ferguson, L., Campbell, C., Kamatani, Y., Okada, Y., Sisodiya, S. M., Cavalleri, G. L., Koeleman, B. P. C., Lerche, H., Jehi, L., Davis, L. K., Najm, I. M., Palotie, A., Daly, M. J., Busch, R. M., ... Epi25 Consortium (2019). Polygenic burden in focal and generalized epilepsies. Brain, 142(11), 3473-3481. https://doi.org/10.1093/brain/awz292