Experiment
Epilepsy has many causes and comorbidities affecting as many as 4% of people in their lifetime. Both idiopathic and symptomatic epilepsies are highly heritable, but genetic factors are difficult to characterize among humans due to complex disease etiologies.
The authors applied a repeated seizure model to a genetic reference population known as the Hybrid Mouse Diversity Panel (HMDP), following seizure susceptibility over a 36 day period. Genome-wide association mapping was carried out using EMMA, a statistical test for association mapping that can correct for genetic relatedness due to population structure. Daily generalized seizure threshold (GST) response differences (in seconds) among HMDP mice were tested for association with 105 SNPs having minor allele frequencies >0.05.
Day 1 GST values among HMDP strains were associated with SNPs on mouse chromosome 1 that overlapped with the previously designated QTL Szs1 (Ferraro et al. 2004; Chaix et al. 2007). However, this QTL, in addition to another on chromosome 5 near Szs6 and a novel locus on mouse chromosome 7, did not reach the genome-wide significance cutoff.
Chromosome 4 GWAS associations were detected at two distinct time points and locations during the repeated-flurothyl seizure model. The authors first detected a locus with maximal effect (-logP = 2.29 x 10^-7) at rs32914632 near 138 Mb on chromosome 4 in the 6 day GST data, while retest GST had associations distal to this region
that were highest (-logP = 6.53 x 10^-7) at rs32163108 near 150 Mb on chromosome 4. Based on this information, the authors designated the retest GST association as epileptogenesis susceptibility factor 1 (Esf1) - a novel seizure susceptibility locus that is dependent on prior seizure exposure to manifest its effects.
We assigned QTL nomenclature to each of the top five SNP associations for kindling, GST1, GST6, and retest GST (genome coordinates relative to NCBI Build 37):
Epsf1 (epileptogenesis susceptibility factor 1, kindling) maps to Chr 1 with a peak -logP score of 5.86 x 10^-9 at 174,420,753 bp (rs3707910).
Epsf2 (epileptogenesis susceptibility factor 2, kindling) maps to Chr 1 with a peak -logP score of 5.86 x 10^-9 at 175,151,112 bp (rs8242481).
Epsf3 (epileptogenesis susceptibility factor 3, kindling) maps to Chr 1 with a peak -logP score of 6.06 x 10^-9 at 174,797,513 bp (rs30463665).
Epsf4 (epileptogenesis susceptibility factor 4, kindling) maps to Chr 1 with a peak -logP score of 1.40 x 10^-8 at 176,533,310 bp (rs2020486).
Epsf5 (epileptogenesis susceptibility factor 5, kindling) maps to Chr 1 with a peak -logP score of 1.41 x 10^-8 at 174,239,958 bp (rs30472229).
Epsf6 (epileptogenesis susceptibility factor 6, GST day 1) maps to Chr 1 with a peak -logP score of 3.15 x 10^-6 at 174,420,753 bp (rs3707910).
Epsf7 (epileptogenesis susceptibility factor 7, GST day 1) maps to Chr 1 with a peak -logP score of 3.15 x 10^-6 at 175,151,112 bp (rs8242481).
Epsf8 (epileptogenesis susceptibility factor 8, GST day 1) maps to Chr 1 with a peak -logP score of 4.22 x 10^-6 at 174,455,423 bp (rs31561177).
Epsf9 (epileptogenesis susceptibility factor 9, GST day 1) maps to Chr 7 with a peak -logP score of 4.61 x 10^-6 at 87,409,991 bp (rs4226715).
Epsf10 (epileptogenesis susceptibility factor 10, GST day 1) maps to Chr 1 with a peak -logP score of 4.98 x 10^-6 at 174,239,958 bp (rs30472229).
Epsf11 (epileptogenesis susceptibility factor 11, GST day 6) maps to Chr 4 with a peak -logP score of 2.29 x 10^-7 at 138,646,868 bp (rs32914632).
Epsf12 (epileptogenesis susceptibility factor 12, GST day 6) maps to Chr 4 with a peak -logP score of 5.93 x 10^-7 at 138,129,729 bp (rs32007081).
Epsf13 (epileptogenesis susceptibility factor 13, GST day 6) maps to Chr 4 with a peak -logP score of 6.80 x 10^-7 at 137,042,287 bp (rs27577055).
Epsf14 (epileptogenesis susceptibility factor 14, GST day 6) maps to Chr 4 with a peak -logP score of 9.71 x 10^-7 at 137,353,761 bp (rs8256572).
Epsf15 (epileptogenesis susceptibility factor 15, GST day 6) maps to Chr 4 with a peak -logP score of 1.13 x 10^-6 at 138,291,047 bp (rs27575102).
Epsf16 (epileptogenesis susceptibility factor 16, GST retest) maps to Chr 4 with a peak -logP score of 6.53 x 10^-7 at 150,729,074 bp (rs32163108).
Epsf17 (epileptogenesis susceptibility factor 17, GST retest) maps to Chr 4 with a peak -logP score of 7.71 x 10^-7 at 150,886,138 bp (rs32757832).
Epsf18 (epileptogenesis susceptibility factor 18, GST retest) maps to Chr 4 with a peak -logP score of 1.11 x 10^-6 at 150,659,779 bp (rs13478053).
Epsf19 (epileptogenesis susceptibility factor 19, GST retest) maps to Chr 4 with a peak -logP score of 1.97 x 10^-6 at 150,681,054 bp (rs32590839).
Epsf20 (epileptogenesis susceptibility factor 20, GST retest) maps to Chr 4 with a peak -logP score of 2.26 x 10^-6 at 150,745,317 bp (rs32180816).
Using systems genetics, the authors identified four candidate genes that are differentially expressed between C57BL/6J and DBA/2J inbred strains close to Esf16-20 that may act individually or as a coordinated response to the neuronal stress of seizures. These four candidate genes are: Camta1, Park7, Per3, and Vamp3.
The authors also found that the DBA/2J allele of the Szs1 locus influences Esf16-20 effects.
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