Royal College of Surgeons in Ireland
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Polygenic burden in focal and generalized epilepsies

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journal contribution
posted on 2021-05-04, 12:13 authored by Costin Leu, Remi Stevelink, Alexander W Smith, Slavina B Goleva, Masahiro Kanai, Lisa Ferguson, Ciaran Campbell, Yoichiro Kamatani, Yukinori Okada, Sanjay M Sisodiya, Gianpiero CavalleriGianpiero Cavalleri, Bobby PC Koeleman, Holger Lerche, Lara Jehi, Lea K Davis, Imad M Najm, Aarno Palotie, Mark J Daly, Robyn M Busch, Epi25 Consortium, Dennis Lal
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 Japanese-ancestry 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.


National Heart, Lung, and Blood Institute (NHLBI)

NHGRI grant UM1 HG008895



The original article is available at This article has an Erratum that can be found at

Published Citation

Leu C, Stevelink R, Smith AW, Goleva SB, Kanai M, Ferguson L, Campbell C, Kamatani Y, Okada Y, Sisodiya SM, Cavalleri GL, Koeleman BPC, Lerche H, Jehi L, Davis LK, Najm IM, Palotie A, Daly MJ, Busch RM; Epi25 Consortium, Lal D. Polygenic burden in focal and generalized epilepsies. Brain. 2019;142(11):3473-3481.

Publication Date

14 October 2019

PubMed ID



  • FutureNeuro Centre
  • School of Pharmacy and Biomolecular Sciences

Research Area

  • Neurological and Psychiatric Disorders


Oxford University Press (OUP)


  • Published Version (Version of Record)