Epilepsy subtype-specific copy number burden observed in a genome-wide study of 17 458 subjects

Abstract

Cytogenic testing is routinely applied in most neurological centres for severe paediatric epilepsies. However, which characteristics of copy number variants (CNVs) confer most epilepsy risk and which epilepsy subtypes carry the most CNV burden, have not been explored on a genome-wide scale. Here, we present the largest CNV investigation in epilepsy to date with 10 712 European epilepsy cases and 6746 ancestry-matched controls. Patients with genetic generalized epilepsy, lesional focal epilepsy, non-acquired focal epilepsy, and developmental and epileptic encephalopathy were included. All samples were processed with the same technology and analysis pipeline. All investigated epilepsy types, including lesional focal epilepsy patients, showed an increase in CNV burden in at least one tested category compared to controls. However, we observed striking differences in CNV burden across epilepsy types and investigated CNV categories. Genetic generalized epilepsy patients have the highest CNV burden in all categories tested, followed by developmental and epileptic encephalopathy patients. Both epilepsy types also show association for deletions covering genes intolerant for truncating variants. Genome-wide CNV breakpoint association showed not only significant loci for genetic generalized and developmental and epileptic encephalopathy patients but also for lesional focal epilepsy patients. With a 34-fold risk for developing genetic generalized epilepsy, we show for the first time that the established epilepsy-associated 15q13.3 deletion represents the strongest risk CNV for genetic generalized epilepsy across the whole genome. Using the human interactome, we examined the largest connected component of the genes overlapped by CNVs in the four epilepsy types. We observed that genetic generalized epilepsy and non-acquired focal epilepsy formed disease modules. In summary, we show that in all common epilepsy types, 1.5-3% of patients carry epilepsy-associated CNVs. The characteristics of risk CNVs vary tremendously across and within epilepsy types. Thus, we advocate genome-wide genomic testing to identify all disease-associated types of CNVs.

Keywords: copy number variation; developmental and epileptic encephalopathy; epilepsy; focal epilepsy; genetic generalized epilepsy.

Figure 1

Global burden of CNV by overall length across four epilepsy types. Rare CNV burden observed in the different epilepsy types is shown for (A) deletions and (B) duplications. Odds ratios (OR) and P-values were calculated using a binomial logistic regression for rare CNVs with sex as a covariate in three different categories (overall genomic sequence loss in one individual of >2 Mb, 500 kb–2 Mb and <500 kb). UE = unclassified epilepsies; *P-values surpassing the Bonferroni multiple testing for 30 tests cut-off (*P < 2.1 × 10⁻³).

Figure 2

The global burden of deletions across different gene sets, hotspot regions and non-coding regions in four different epilepsy phenotypes. Common deletion burden was elucidated for epilepsy hotspot regions (Carvill and Mefford, 2013) and rare (<1% frequency) deletion burden was elucidated for all other gene lists (Category). Odds ratios (OR) and P-values were calculated using a binomial regression for common CNVs and a binomial regression for rare CNVs with sex as a covariate. CNVs are defined as ‘genic’ if they overlap 80% of a gene. Notably, not all individuals carry a CNV. (Results of CNV burden in neurodevelopmental disorder hotspots and genes are not shown because of very small sample sizes and no significance; results of duplication burden are shown in Supplementary Fig. 4.) When they exceed a specified limit, 95% CIs are clipped to arrows. *P-values surpassing the Bonferroni multiple testing for 36 tests cut-off (*P < 1.4 × 10⁻³).

Figure 3

Global burden of likely pathogenic CNVs across four different epilepsy phenotypes. Likely pathogenic CNVs were defined as rare deletions in neurodevelopmental disorders and epilepsy genes and in recurrent epilepsy hotspots and duplications of 16p11.2, odds ratios (OR) and P-values were calculated using a binomial logistic regression for rare CNVs with sex as a covariable. Genic CNVs are defined as those that overlap 80% of any exon of a known protein-coding gene. *P values surpassing the Bonferroni multiple testing for four tests cut-off (*P < 0.0125).

Figure 4

Genome-wide CNV breakpoint association. Manhattan plot displaying the −log10 deviance P-value for (A) genome-wide deletion breakpoint association for DEE, GGE, LFE, and NAFE; and (B) genome-wide duplication breakpoint association for DEE, GGE, LFE, and NAFE. P-value cut-offs corresponding to correction for 46 846 tests at 1.0673 × 10⁻⁶ are highlighted in red. Loci significant after multiple test correction in the appropriate epilepsy type are labelled.