Abstracts

Rationale: Somatic mutations are increasingly recognized as an underlying cause for malformations of cortical development ranging from small focal cortical dysplasias to large hemispheric malformations. However, somatic mutation detection in brain surgery tissue is not yet part of routine clinical care and the implications on therapy and outcome are unknown. Many previous studies have used historical samples and banked tissues, making it difficult estimate the frequency of relevant somatic mutations and the role of somatic mutation detection in the setting of epilepsy surgery and post-surgical epilepsy care. In our study, we aimed to determine the burden and nature of somatic mutations in children with epilepsy undergoing epilepsy surgery in a prospective cohort. Methods: We prospectively recruited pediatric patients with intractable epilepsy undergoing epilepsy surgery at the Children’s Hospital of Philadelphia and harvested various regions of affected brain tissue per resected sample that were processed using a dedicated biobanking protocol. After histological review, we performed whole-genome sequencing on the most severely affected brain tissue specimen per sample (60x whole genome coverage) and on DNA samples derived from whole blood (30x whole genome coverage). We used the CAVATICA data analysis platform using GATK and MuTect2 for detection of somatic mutations and analyzed variants in genes implicated in epilepsy-related somatic mutations including components of the mTOR pathway, as well as known genetic etiologies for human epilepsies. Results: Our final cohort of consecutive patients who consented for our prospective study included 12 individuals with a median age of 9 years (range: 21 months-17 years).  Clinical diagnoses in this cohort included focal cortical dysplasia (FCD, n=9), Rasmussen encephalitis (n=2), and Aicardi syndrome (n=1). In a patient with FCD 2b, screening for somatic mutations identified a low-level (10%) mosaic c.6644C>T (p.Ser2215Phe) MTOR variant a known pathogenic variant. We did not identify other somatic mutations in components of the MTOR pathway, known genetic etiologies, or known pathogenic variants in the ClinVar database. Conclusions: In our study, we demonstrate the feasibility of a systematic detection of somatic mutations in children with intractable epilepsy undergoing resective brain surgery. By using a Cavatica and Kids First cloud-based data analysis and sharing platform, this pipeline is rapid and scalable. The identification of a somatic mutation in MTOR in a patient with FCD IIb reinforces that somatic mutations are frequent enough to be routinely identified in individuals undergoing epilepsy surgery, arguing for the implementation of somatic mutation detection into routine care. Funding: University of Pennsylvania McCabe Award -- PI: Benjamin Kennedy