Elsevier

The Lancet Neurology

Volume 16, Issue 2, February 2017, Pages 135-143
The Lancet Neurology

Articles
Ultra-rare genetic variation in common epilepsies: a case-control sequencing study

https://doi.org/10.1016/S1474-4422(16)30359-3Get rights and content

Summary

Background

Despite progress in understanding the genetics of rare epilepsies, the more common epilepsies have proven less amenable to traditional gene-discovery analyses. We aimed to assess the contribution of ultra-rare genetic variation to common epilepsies.

Methods

We did a case-control sequencing study with exome sequence data from unrelated individuals clinically evaluated for one of the two most common epilepsy syndromes: familial genetic generalised epilepsy, or familial or sporadic non-acquired focal epilepsy. Individuals of any age were recruited between Nov 26, 2007, and Aug 2, 2013, through the multicentre Epilepsy Phenome/Genome Project and Epi4K collaborations, and samples were sequenced at the Institute for Genomic Medicine (New York, USA) between Feb 6, 2013, and Aug 18, 2015. To identify epilepsy risk signals, we tested all protein-coding genes for an excess of ultra-rare genetic variation among the cases, compared with control samples with no known epilepsy or epilepsy comorbidity sequenced through unrelated studies.

Findings

We separately compared the sequence data from 640 individuals with familial genetic generalised epilepsy and 525 individuals with familial non-acquired focal epilepsy to the same group of 3877 controls, and found significantly higher rates of ultra-rare deleterious variation in genes established as causative for dominant epilepsy disorders (familial genetic generalised epilepsy: odd ratio [OR] 2·3, 95% CI 1·7–3·2, p=9·1 × 10−8; familial non-acquired focal epilepsy 3·6, 2·7–4·9, p=1·1 × 10−17). Comparison of an additional cohort of 662 individuals with sporadic non-acquired focal epilepsy to controls did not identify study-wide significant signals. For the individuals with familial non-acquired focal epilepsy, we found that five known epilepsy genes ranked as the top five genes enriched for ultra-rare deleterious variation. After accounting for the control carrier rate, we estimate that these five genes contribute to the risk of epilepsy in approximately 8% of individuals with familial non-acquired focal epilepsy. Our analyses showed that no individual gene was significantly associated with familial genetic generalised epilepsy; however, known epilepsy genes had lower p values relative to the rest of the protein-coding genes (p=5·8 × 10−8) that were lower than expected from a random sampling of genes.

Interpretation

We identified excess ultra-rare variation in known epilepsy genes, which establishes a clear connection between the genetics of common and rare, severe epilepsies, and shows that the variants responsible for epilepsy risk are exceptionally rare in the general population. Our results suggest that the emerging paradigm of targeting of treatments to the genetic cause in rare devastating epilepsies might also extend to a proportion of common epilepsies. These findings might allow clinicians to broadly explain the cause of these syndromes to patients, and lay the foundation for possible precision treatments in the future.

Funding

National Institute of Neurological Disorders and Stroke (NINDS), and Epilepsy Research UK.

Introduction

Next generation sequencing has proven successful in identifying genetic contributions to rare Mendelian disorders and cancers,1, 2 creating widespread optimism that treatments can be targeted to underlying causes of disease.3 Epilepsy is a common complex disease that is emerging as a group of disorders with similar precision medicine opportunities.4 Unlike in many common diseases, epilepsy genetics research is identifying the genes responsible and also the genetic variants contributing to disease in individual patients. This individual precision is most apparent in the discoveries of the role of de novo mutations in the epileptic encephalopathies.5, 6

Traditional heritability studies of common epilepsies consistently show strong genetic effects in non-acquired focal epilepsy and in genetic generalised epilepsy, with both shared and distinct genetic contributions to these broadly defined epilepsies.7, 8 Two important unresolved questions are the extent to which the genes responsible for rare, severe epilepsies contribute to common epilepsies, and whether, as in the rare epilepsies, genetic risk arises primarily from ultra-rare variants of large effect including de novo mutations,5, 6 or from a constellation of common variants each conferring small or modest effect.9, 10, 11, 12, 13

Exome sequencing of large cohorts followed by genome-wide collapsing analyses provide a non-hypothesis driven approach to discovering novel disease genes and better understanding of the overall contribution of ultra-rare genetic variation to disease.14 We aimed to assess the contribution of ultra-rare genetic variation to common epilepsies while controlling for background variation in the general population.

Research in context

Evidence before this study

The genetic underpinnings of common epilepsies are largely unknown, especially the relative contributions of common variants of small effect size versus rare variants of large effect, for which opportunities for novel therapeutic strategies might be greater. We searched PubMed with the terms “exome sequencing” and “common epilepsy” for reports published before June 28, 2016, with no language restrictions. There were no reports of exome sequencing of large case collections of common complex epilepsies. Although exome sequencing studies have been successful in implicating numerous genes and finding the relevant mutations for individuals with rare, severe, paediatric epilepsies, including epileptic encephalopathies, estimating the risk contribution from the ultra-rare protein-coding variants has been less clear for many of the common epilepsy syndromes.

Added value of this study

We used whole exome sequencing on a large collection of data from patients with one of two common epilepsy syndromes, genetic generalised epilepsy and non-acquired focal epilepsy, to search for ultra-rare deleterious qualifying variants, and compared the qualifying variant rates found in these cases to background rates estimated from sequenced controls. Among familial index cases sampled from the common epilepsies, we found a significant excess of ultra-rare deleterious variation within known epileptic encephalopathy genes. We also show that the epilepsy risk signal observed in the known epilepsy genes is accounted for by the ultra-rare class of variants that are absent among large reference control cohorts, such as the Exome Aggregate Consortium and Exome Variant Server. Variants in known epilepsy genes that were predicted to be deleterious, but found at very low frequencies in the population reference cohorts, showed no evidence of contribution to epilepsy risk.

Implications of all the available evidence

The present findings provide three key conclusions for our understanding of the common epilepsies. First, the identification of significant enrichment of ultra-rare deleterious variants in established epilepsy genes show that there are risk associations that can be identified through this methodology. Second, we showed that the precision medicine framework that is emerging for rare epilepsies can be expected to find applications also in more common epilepsies. Finally, we showed that risk in the common complex forms of epilepsy is associated with the rarest variants in the human population, providing the clearest insight available at present into the genetic variants underlying this common complex disorder. Further research is warranted to translate these findings into clinical practice.

Section snippets

Study design and participants

For this case-control study, participants with familial or sporadic non-acquired focal epilepsy or familial genetic generalised epilepsy were recruited between Nov 26, 2007, and Aug 2, 2013, through the international Epilepsy Phenome/Genome Project and Epi4K collaborations (appendix), as previously described.15 The patient samples were sequenced between Feb 6, 2013, and Aug 18, 2015, by the Institute for Genomic Medicine (Columbia University, New York, NY, USA). To be clinically classified as

Results

We sequenced the exomes of 1827 patients with epilepsy. Of these, 640 are unrelated individuals of European ancestry with a diagnosis of familial genetic generalised epilepsy; 525 are unrelated individuals of European ancestry with a diagnosis of familial non-acquired focal epilepsy; an additional 662 individuals reported sporadic non-acquired focal epilepsy. We compared these three groups of patients with epilepsy with 3877 controls, who were unrelated individuals of European ancestry with no

Discussion

Our study shows that genes established as responsible for familial and rare severe epilepsies are also associated with common epilepsies. In our analysis of a cohort of individuals with familial non-acquired focal epilepsy, we found that five established epilepsy genes (DEPDC5, LGI1, PCDH19, SCN1A, and GRIN2A) occupy the top five positions of ascending p value order for the 18 668 tested protein-coding genes (figure 2) and after correcting for background variation, the population attributable

References (28)

  • JC Darnell et al.

    FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism

    Cell

    (2011)
  • C Gilissen et al.

    Unlocking Mendelian disease using exome sequencing

    Genome Biology

    (2011)
  • EA Collisson et al.

    What are we learning from the cancer genome?

    Nat Rev Clin Oncol

    (2012)
  • A roadmap for precision medicine in the epilepsies

    Lancet Neurol

    (2015)
  • AT Berg et al.

    Revised terminology and concepts for organization of seizures and epilepsies: report of the ILAE Commission on Classification and Terminology, 2005–2009

    Epilepsia

    (2010)
  • De novo mutations in epileptic encephalopathies

    Nature

    (2013)
  • De novo mutations in synaptic transmission genes including DNM1 cause epileptic encephalopathies

    Am J Hum Genet

    (2014)
  • L Vadlamudi et al.

    Genetics of epilepsy: The testimony of twins in the molecular era

    Neurology

    (2014)
  • AL Peljto et al.

    Familial risk of epilepsy: a population-based study

    Brain

    (2014)
  • ET Cirulli et al.

    Uncovering the roles of rare variants in common disease through whole-genome sequencing

    Nat Rev Genet

    (2010)
  • DB Goldstein

    Common genetic variation and human traits

    NEJM

    (2009)
  • Electronic address e-auea. Genetic determinants of common epilepsies: a meta-analysis of genome-wide association studies

    Lancet Neurol

    (2014)
  • TA Manolio et al.

    Finding the missing heritability of complex diseases

    Nature

    (2009)
  • G Gibson

    Rare and common variants: twenty arguments

    Nat Rev Genet

    (2011)
  • Cited by (171)

    View all citing articles on Scopus

    Members and affiliations listed at the end of this paper.

    View full text