Abstract
ObjectiveThe Genetic Absence Epilepsy Rats from Strasbourg (GAERS) are an inbreed Wistar rat strain widely used as a model of genetic generalised epilepsy with absence seizures. As in humans, the genetic architecture that results in genetic generalized epilepsy in GAERS is poorly understood. Here we present the strain-specific variants found among the epileptic GAERS and their related Non-Epileptic Control (NEC) strain. The GAERS and NEC represent a powerful opportunity to identify neurobiological factors that are associated with the genetic generalised epilepsy phenotype.MethodsWe performed whole genome sequencing on adult epileptic GAERS and adult NEC rats, a strain derived from the same original Wistar colony. We also generated whole genome sequencing on four double-crossed (GAERS with NEC) F2 selected for high-seizing (n = 2) and non-seizing (n = 2) phenotypes.ResultsSpecific to the GAERS genome, we identified 1.12 million single nucleotide variants, 296.5K short insertion-deletions, and 354 putative copy number variants that result in complete or partial loss/duplication of 41 genes. Of the GAERS-specific variants that met high quality criteria, 25 are annotated as stop codon gain/loss, 56 as putative essential splice sites, and 56 indels are predicted to result in a frameshift. Subsequent screening against the two F2 progeny sequenced for having the highest and two F2 progeny for having the lowest seizure burden identified only the selected Cacna1h GAERS-private protein-coding variant as exclusively co-segregating with the two high-seizing F2 rats.SignificanceThis study highlights an approach for using whole genome sequencing to narrow down to a manageable candidate list of genetic variants in a complex genetic epilepsy animal model, and suggests utility of this sequencing design to investigate other spontaneously occurring animal models of human disease.
Highlights
The genetic generalised epilepsies (GGE) comprise a group of epileptic disorders that include absence seizures as one of the classical seizure phenotypes [1,2,3] with evidence that some cases might be explained by a complex polygenic mode of inheritance [4,5,6,7,8,9,10]
After accounting for PCR duplicates and reads that did not align to the reference genome, in the Genetic Absence Epilepsy Rats from Strasbourg (GAERS), approximately 23.48 million reads (37.6 Gb) were mapped to the Brown Norway (BN) reference genome (RGSC v3.4) using BWA [26] and variant calling using samtools [27]
Both strains originated from the same outbred Wistar rat colony, which selectively bred based on the presence (GAERS) or absence (NEC) of spontaneously arisen absence seizures and the corresponding spike-and-wave discharge (SWD) signatures
Summary
The genetic generalised epilepsies (GGE) comprise a group of epileptic disorders that include absence seizures as one of the classical seizure phenotypes [1,2,3] with evidence that some cases might be explained by a complex polygenic mode of inheritance [4,5,6,7,8,9,10]. Analogous to human absence epilepsy, GAERS have spontaneously occurring SWDs that start and end abruptly on a normal EEG background [5, 12, 13]. GAERS exhibit a similar pharmacological profile when compared to human absence seizures, being suppressed or aggravated by the same anti-epileptic drugs [12,13,14,15,16,17,18]. Extensive cross breeding studies have demonstrated that the GAERS epileptic phenotype is likely to be complex and polygenic [12]. We have published the missense (R1584P) variant in the low-threshold T-type calcium channel CaV3.2 gene (Cacna1h) as accounting for up to 33% of variance for the percentage of time in seizures and the number of seizures based on data from F2 progeny of a cross between NEC and GAERS rats [23, 24]
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