Rare coding variants in genes encoding GABAA receptors in genetic generalised epilepsies: an exome-based case-control study

Abstract

EuroEPINOMICS (European Science Foundation through national funding organisations), Epicure and EpiPGX (Sixth Framework Programme and Seventh Framework Programme of the European Commission), Research Unit FOR2715 (German Research Foundation and Luxembourg National Research Fund).

Ultra-rare genetic variation in the epilepsies: a whole-exome sequencing study of 17,606 individuals

“…None of the gene sets was enriched for putatively neutral variation, except for a slightly elevated synonymous burden in GABA A receptor genes ( Table S8 ). These results support a recent finding where rare missense variation in GABA A receptor genes conferred a significant risk to GGE 18 , and together implicate the relative importance and involvement of damaging missense variants in abnormal inhibitory neurotransmission in both rare and common epilepsy types.…”

“…Among brain-enriched genes—those defined as genes with at least a 2-fold increase in expression in brain tissues relative to their average expression across tissues based on GTEx data 32 —both protein-truncating and damaging missense (MPC≥2) URVs were significantly enriched in epilepsy cases versus controls, and the missense burden was much higher than the PTV burden ( Figure S15 ). We then investigated the burden in four smaller gene sets previously implicated as mechanisms driving the etiology of epilepsy; these included 19 genes encoding GABA A receptor subunits, 113 genes involved in GABAergic pathways, 34 genes encoding excitatory receptors (ionotropic glutamate receptor subunits and nicotinic acetylcholine receptor subunits), and 86 voltage-gated cation channel genes (e.g., sodium, potassium, calcium—full list in Table S6 ) 18 . We discovered that, relative to damaging missense variants, the distribution of PTVs in most of these gene sets did not differ significantly between epilepsy cases and controls ( Figure 2A ; Table 1 ).…”

“…The inclusion of overall variant count as a covariate—which tracks with ancestry—made our test conservative but allows for better control of residual population stratification not captured by PCs, and effectively reduces inflation of signals in synonymous variants ( Figure S11 ). We collected and tested eleven different gene sets, including constrained genes, brain-enriched genes, and genes reported to be associated with epilepsy or epilepsy-related mechanisms 9; 17;18; 32; 33 ( Table S6 ). Unlike the gene-based burden tests, because most of the gene-set tests were not independent, we used a false discovery rate (FDR) correction for multiple testing that accounted for the number of functional categories (5), gene sets (11) and epilepsy phenotypes (4), totaling 220 tests, and defined a significant enrichment at FDR < 0.05.…”

“…The common subgroups of epilepsy, broadly comprising genetic generalized epilepsy (GGE) and non-acquired focal epilepsy (NAFE), account for a major proportion of all incident epilepsies 2; 13 and have been shown robust heritability in twin, family, and genome-wide association studies (GWAS) 4;14-16 . Disappointingly, only a limited number of genes had been discovered to date for the common epilepsies, mostly from rare monogenic families with focal epilepsies, and attempts to identify clear risk genes for GGE have been least successful 12;17;18 . In most cases, especially for non-familial onset, the specific pathogenic variants are not yet known, and gene findings from small-scale studies have often not been reproducible 19-21 .…”

“…Many of the identified genes are associated with a spectrum of mild to severe epilepsies, showing phenotypic pleiotropy or variable expressivity, and most of the electroclinical syndromes have diverse genetic causes 10; 22 . Two recent studies using whole-exome sequencing (WES) of hundreds of individuals with common familial epilepsies found an enrichment in ultra-rare genetic variation in genes associated with rare epilepsy syndromes 17 and in missense variants in a group of genes encoding all GABA A receptors, the most important neurotransmitter receptors for neuronal inhibition in the mammalian brain 18 . Given the complex genetic architecture of the epilepsies, it is therefore critical to pinpoint the distinct and overlapping genetic risk factors underlying different groups of epilepsy on a scale much larger than previous sequencing studies and beyond familial cases.…”