Exome sequencing followed by large-scale genotyping fails to identify single rare variants of large effect in idiopathic generalized epilepsy

Abstract

Idiopathic generalized epilepsy (IGE) is a complex disease with high heritability, but little is known about its genetic architecture. Rare copy-number variants have been found to explain nearly 3% of individuals with IGE; however, it remains unclear whether variants with moderate effect size and frequencies below what are reliably detected with genome-wide association studies contribute significantly to disease risk. In this study, we compare the exome sequences of 118 individuals with IGE and 242 controls of European ancestry by using next-generation sequencing. The exome-sequenced epilepsy cases include study subjects with two forms of IGE, including juvenile myoclonic epilepsy (n = 93) and absence epilepsy (n = 25). However, our discovery strategy did not assume common genetic control between the subtypes of IGE considered. In the sequence data, as expected, no variants were significantly associated with the IGE phenotype or more specific IGE diagnoses. We then selected 3,897 candidate epilepsy-susceptibility variants from the sequence data and genotyped them in a larger set of 878 individuals with IGE and 1,830 controls. Again, no variant achieved statistical significance. However, 1,935 variants were observed exclusively in cases either as heterozygous or homozygous genotypes. It is likely that this set of variants includes real risk factors. The lack of significant association evidence of single variants with disease in this two-stage approach emphasizes the high genetic heterogeneity of epilepsy disorders, suggests that the impact of any individual single-nucleotide variant in this disease is small, and indicates that gene-based approaches might be more successful for future sequencing studies of epilepsy predisposition.

Figure 1

Overview of the Study Design

Figure 2

Power for Detecting an Epilepsy-Susceptibility Variant in This Study The detectable relative risk of an IGE-susceptibility variant across a range of MAFs in the sequencing phase of this study (blue line) is compared to that of the follow-up genotyping phase of this study (red line). To be significant, associations must have a p value below 6 × 10⁻⁷, which is equivalent to p < 0.05 when we correct for all 87,255 high-quality, functional variants that were annotated as functional and had a control MAF < 5% in the sequencing study. Power calculations were performed with the CaTS-Power Calculator.

Figure 3

Quantile-Quantile Plot Shows No Evidence of Population Stratification A quantile-quantile plot of transformed p values (black dots) against the expected transformed p values for variants with at least six alleles represented in the study population. The red line indicates the expectation under the null model of no effect on risk.