  In the context of pharmacogenomics, whole genome sequencing provides a
powerful approach for identifying correlations between response variability to
specific drugs and genomic polymorphisms in a population, in an unbiased
manner. In this study, we employed whole genome sequencing of DNA samples from
patients showing extreme response (n=72) and non-response (n=27) to the
antiepileptic drug levetiracetam, in order to identify genomic variants that
underlie response to the drug. Although no common SNP (MAF>5%) crossed the
conventional genome-wide significance threshold of 5e-8, we found common
polymorphisms in genes SPNS3, HDC, MDGA2, NSG1 and RASGEF1C, which collectively
predict clinical response to levetiracetam in our cohort with ~91% predictive
accuracy. Among these genes, HDC, NSG1, MDGA2 and RASGEF1C are potentially
implicated in synaptic neurotransmission, while SPNS3 is an atypical solute
carrier transporter homologous to SV2A, the known molecular target of
levetiracetam. Furthermore, we performed gene- and pathway-based statistical
analysis on sets of rare and low-frequency variants (MAF<5%) and we identified
associations between the following genes or pathways and response to
levetiracetam: a) genes PRKCB and DLG2, which are involved in glutamatergic
neurotransmission, a known target of anticonvulsants, including levetiracetam;
b) genes FILIP1 and SEMA6D, which are involved in axon guidance and modelling
of neural connections; and c) pathways with a role in synaptic
neurotransmission, such as WNT5A-dependent internalization of FZD4 and
disinhibition of SNARE formation. In summary, our approach to utilise whole
genome sequencing on subjects with extreme response phenotypes is a feasible
route to generate plausible hypotheses for investigating the genetic factors
underlying drug response variability in cases of pharmaco-resistant epilepsy.
